Short answer is yes, but not many. Japanese studies estimate that about 700-800 men stayed in French Indochina to fight against French colonial forces.
In the case of Vietnam we know of a number of specific cases. For example, there were Igawa Sei (major, Imperial Japanese Army) and Nakahara Mitsunobu (Lieutenant, IJA). Igawa was in the cavalry, so he learned French (instead of German), and after being sent to Vietnam cooperated with the Vietcong. At the end of the war, he unlocked the room that stored confiscated French weapons at Fue and told his troops to leave, which allowed the Vietcong to take those weapons. Apparently he worked closely with Nguyen Son (who had participated in the Long March with the Chinese Communists and eventually become a general in the Vietnamese Army). Igawa also translated the Japanese army infantry manual into French so that the Vietnamese could read it and imparted military training to the Vietcong. He died in an ambush by French forces.
Nakahara was Igawa's subordinate at the end of the war, and after Igawa's death helped Ngueyn Son found the Quang Ngai military academy. This military school was in the middle of a sugar cane field with only 10 buildings, 4 instructors and 4 sub-instructors, with 1 military doctor, all of whom were Japanese. About 400 students, divided into 4 teams of 100 students, studied there. The students graduated in 6 months so it had a high turn over and many Vietnamese leaders would emerge from this school.
Some of these Japanese soldiers died in combat, a few returned to Japan, but also a significant number became Vietnamese. Overall, I agree with Goscha who wrote that Japanese technical transfer is important because it bridged the gap between 1945 and 1950 and gave the Vietnamese know-how in fighting against the French at the time when the Vietnamese were at their weakest but had the greatest need for it.
(After 1950, it would be Communist Chinese advisers that would be important.)
There's more but you can read more of this in Japanese published in 2005 in http://nippon.zaidan.info/seikabutsu/2005/01036/pdf/0001.pdf
and in English in Christopher Goscha's chapter "Belated Asian Allies" in Marilyn Young and Robert Buzzanco (eds) A Companion to the Vietnam War (1988), p.37-56. http://books.google.com/books?id=WsULqb6k0BoC&printsec=frontcover&dq=google+books+a+companion+to+the+vietnam+war&hl=en&sa=X&ei=tcp8U_23CMe3sASGsoHwDA&ved=0CD0Q6AEwAA#v=onepage&q=google%20books%20a%20companion%20to%20the%20vietnam%20war&f=false
Edit: I don't know too much about Indonesia but Kalibata Heroes Cemetery wikipedia entry has more on this topic too. According to the information there, more Japanese fought for Indonesian independence than for Vietnamese independence. I hope someone who knows about Indonesia can post more on it.
Following the end of the second world war British troops moved into Vietnam and started running a remarkably successful campaign (operation MASTERDOM) based upon the tactical employment of combined British/Indian army and re-armed Japanese army combined patrols, aiming at the re-establishment of French colonial power in far east Asia. The difficulties that this country would face in the future were beginning to surface due to their refusal to surrender to the French, due to highly successful British military operations, the speedy French collapse and the emphasis upon nationalism as a component to Viet minh policy. Viet minh forces would only offer their surrender to British forces, who in turn handed over power to a French government perceived as weak and powerless.
Details are difficult to obtain however due to the complex nature of the fighting, with limited British and French forces involved, a larger Indian army deployment at the end of the British raj limiting interest in India and the employment of re-armed Japanese servicemen outside of Japanese service. the consequent difficulties resulting from language have resulted in limited research and appreciation of methods.
Many officers in the Republic Of Korea (South) Army were in the Imperial Japanese Army.
I Wunjun (in Japanese)
An Heihan (in Japanese)
Che Pyondok (in Japanese)
Bek Honsok (in Japanese)
Kim Jonnyom (in Japanese)