As verbs the difference between instruct and indoctrinate is that instruct is ( label ) to teach by giving instructions while indoctrinate is to teach with a biased, one-sided or uncritical ideology.

Indoctrinate alone of these words [in the teach category], suggests the inculcation of propaganda or prejudices rather than unbiased knowledge: parents who indoctrinate their children with race hatred; schools that unconsciously indoctrinate their students with middle-class values.

As Verb the main difference between Instruct and Indoctrinate is that Instruct is give instructions or directions for some task while Indoctrinate is teach doctrines to; teach uncritically

indoctrinate - Referring to the process of teaching or instructing someone in a particular ideology or belief system, often with a negative connotation. - Describing the act of brainwashing or manipulating someone into accepting a certain set of beliefs or ideas.