It indeed was.

It was used on criminals of the highest degree, often murderers. Knowledge of crucifixion as a method of execution was most likely influenced if not heavily informed by Christianity.

It was also notably used to execute Christians and missionaries, throughout most of the Edo Period (16th to 19th century). Christianity was heavily repressed and was outlawed during this time until the early 1800s. Christians were regularly persecuted and summarily executed for their faith.

This persecution of Christians is symbolized in the Japanese word 踏み絵fumi-e which means 'trample picture'.

This is because the Tokugawa Shogunate established a test at many bridges, roads, gates, and border crossings. The test consisted of a tablet of an immaculately carved or forged image of Mary or Jesus. Guards would order everyone passing through to step on the tablet and anyone who showed hesitation or refused would be declared a Christian and arrested.

Many were then sent to Nagasaki, which was notable as the one port that foreigners were allowed to dock and do trade at.

The most famous Christian suppression is probably at Nagasaki, where dozens of priests and Christians, including children, were executed, though it was often by beheading and not crucifixion.

Today the word 踏み絵fumi-e is often used as a metaphor for a test of your principles or faith. It can also be used as a metaphor for a hard choice between ideals or values and pragmatism or more basic needs, like living.