I recently learned that this occurred under his administration but I haven’t found anything detailing if he knew about it and what his reactions were to it.
Edit:
As a follow up, what was Lincoln’s views on natives like during the civil war? What was his native America policy? Did he ever want to reform the way they were treated?
Lincoln, as a white man from the 19th century, had his biases and flaws. One of these is how he conceived of the American West mostly as land for White men to develop, and his rather patronizing and condescending aptitude towards Indians.
Now, Lincoln was no "Indian-hater", but he devoted little time to their issues. This was, to a certain degree, understandable. After all, the Union was going through its supreme trial, and Lee's rebels represented a more immediate threat. Lincoln did try to implement a fair policy, or at least what he thought was fair. A compassionate man, he prohibited General John Pope from carrying out any executions without his approval after the General put down a Sioux uprising in Minnesota. Pope recommended the trial of 1.500 captured men, women and children, and he went as far as declaring that “It is my purpose utterly to exterminate the Sioux if I have the power to do so. . . . They are to be treated as maniacs or wild beasts.”
Lincoln frankly admitted that he was not well-versed in Indian affairs, telling Chief John Ross that he had "been unable to examine and determine the exact treaty relations between the United States and the Cherokee Nation.” He sent John P. Usher to Minnesota to examine the situation, and sought advice on the matter. Pope returned a list of 303 Sioux men condemned to die, and despite strong pressure to carry out these executions, Lincoln refused. At first, he tried to find some kind of workaround, but Joseph Holt, a judge advocate, told him firmly that it could not be delegated. Lincoln then minociously went through the list of names and details of the trials, and chose 39 men who had been convicted of crimes such as rape and murder. He sent the list to Minnesota, instructing the telegraph operator to be careful "since even a slight error might send the wrong man to his death."
One man was pardoned at the last minute, but the 38 executions still represented the largest mass executions in American history. Instead of praising him for his humanity, most people tended to attack Lincoln for being "soft". Senator Ramsey, who had been Minnesota's governor during the uprising, even said that had Lincoln executed all the men he would have gathered greater majorities during the Minnesota elections. “I could not afford to hang men for votes,” Lincoln replied grimly.
Despite this noteworthy incident, the Lincoln Administration was not characterized by special concern for the Natives and their plight. For example, Lincoln recognized the corruption of the Office of Indian Affairs, and the need to reform it, mentioning that in his annual messages to Congress. But he took no real steps to do so, rewarding political supporters with appointments to the Interior Department (which oversaw the Office), and posts within the Office were given to Republicans as patronage plums. He even instructed Secretary of the Interior Smith to fill all Indian posts with the men recommended by Wisconsin's congressional delegation.
When it came to broader policy, Lincoln thought it necessary to extinguish the “possessory rights of the Indians to large and valuable tracts of land”, and though he wanted to provide for “the welfare of the Indian", he eagerly signed into law bills that made this all but impossible, such as the Homestead Act or the Transcontinental Railway. Both measures promised further encroachment into Indian land, something that Lincoln, who "considered the Indians a barbarous people who were a barrier to progress", welcomed.
Lincoln showed this kind of disregard personally as well. An embarrassing episode took place when he received 14 Indian chiefs in the White House. In the words of Eric Foner, "His remarks were patronizing and illogical". Indeed, he told them that the world was round ("this world is a great, round ball”) and that American success was owed to them being farmers instead of hunters. This, Lincoln said, was the “great difference between this pale-faced people and their red brethren,” adding that “We are not, as a race, so much disposed to fight and kill one another as our red brethren.” A rather ironic statement since the U.S. was then going through its bloodiest war.
Foner concludes that "Lincoln’s Indian policies are depressingly similar to those of virtually every nineteenth-century president", attributing this to his lack of contact with Native Americans and the lack of any national movement or events at the national scale that could change his opinions, as it happened with African-Americans. Overall, the Lincoln Administration had a sorry record in regards to Native American affairs. He recognized that they were often treated unjustly, and did not express the contempt other people did. But he did not pay them much attention and did not undertake any initiatives to actually reform the system or improve their lot.
I cannot find any mention of the Navajo Long Walk in any of my sources, but it's rather likely that Lincoln did not even know about it, and if he did, did not consider it exceptional. Since his sole focus was on the issues of the Civil War, and also because he thought removing Indians was necessary to allow White people to develop the West, it's sadly probable that if he knew of this tragic event he thought it unworthy of mention and intervention. But as I said, I have no sources that focus on this, so let's hope there's somebody else more knowledgeable about the topic.
Sources:
David Herbert Donald's Lincoln biography and Eric Foner's The Fiery Trial dedicate some space to Lincoln's attitudes towards Native Americans and his Administration's policies.
Sorry this has taken me so long. u/Red_Galiray did an excellent job covering Lincoln's role and perspective; so allow me to answer how the Navajo Long Walk did happen. And what happened once members of Washington were aware of just what was going on.
1861 and 1862 were very terrible years for the US. Not only did the southern states rise in rebellion in support of slavery, but western states like Texas did as well. More concerning, Confederate troops claimed the "Arizona Territory" from a section of the then territory of New Mexico. Combined with rumors of Confederate sympathies in Oregon, and tribes like the Choctaw and Cherokee aligning in some part with the Confederacy, the Union was very worried about the possibility of mass uprisings throughout the west, something it's frontier garrisons could have little hope of overcoming.
In response, many commanders were given the expectation to "solve" problems in their areas, with significantly less oversight and resources.
Enter General Carleton, architect of the Long Walk. Carleton had been in charge of the region around the Navajo, and had a frankly terrible relationship with them. The Navajo Wars were a a repeating cycle of Navajo raiding, met with US Army forces, which would result in peace treaties that the Army would then not honor, causing a vicious cycle of conflict.
The Navajo Wars reached their peak as Carleton implemented his plan to send all Navajo, and Apache, to Fort Sumner in Texas. To get the Navajo to go there, he hired Kit Carson, a frontier man, to guide his troops in their war to destroy the Navajo's crops and herds, so they would be forced to surrender to Army forces. Needless to say, his plan was successful.
In Carleton's report of his plan to force the Navajo, wearied from a scorched earth war, to march over three hundred miles to Fort Sumner; he describes the process as "humane" (you can read it here https://en.wikisource.org/wiki/Letter_recommending_removal_of_the_Navajo_to_Bosque_Redondo )
Once at Fort Sumner Carleton significantly mismanaged the Navajo population there. They fought with the Apache, as they were long-time enemies. There were not enough rations for everyone, the soil was of poor quality for farming, and the Fort itself was significantly over-crowded.
I bring this up, because it ties into how the government in Washington viewed the Long Walk, they really didn't know much all about it. And Carleton, it seems, really couldn't care less about the conditions of the Navajo. He thought he was "civilizing" them and converting them. My case and point of how differently someone else at the time would view the Long Walk and it's effects: in 1868, when General Sherman was on his mission from General Grant to end the Indian Wars, he arrived at Fort Sumner.
Sherman was absolutely shocked at the conditions there, comparing it to the infamous Confederate run prison camp, Andersonville. Sherman was absolutely furious. A mixture of this anger, and the Navajo elders speaking with the delegation allowed for a (relatively) lenient treaty for the Navajo.
This is not to white-wash US Government or Army actions during this period. But, there were people in that time, who were far more ruthless and brutal than others.
Recommended Readings:
The above letter
Navajo Long Walk: Tragic Story of a Proud Peoples Force March from Homeland by Joseph Bruchac
Navajo Stories of the Long Walk by Johnson Broderick
Oral history stories of the Long Walk by Anonymous
The Memoirs of General Sherman by William Sherman
And a book to stay very, very, VERY(!) far away from, but keeps being recommended on the topic: The Army and the Navajo: The Bosque Redondo Experiment by Gerald Thompson.