"I don't know if that's necessarily true" means "That might not be true."
You can use this phrase to politely disagree with a statement that someone has made. For example:
A: You definitely need to have a degree in Computer Science to get a job as a computer programmer, right?
B: I don't know if that's necessarily true.
This phrase is more polite than "That's not true" or "That's wrong" because it leaves open the possibility that what the person has said might be true. "I don't know if..." and "necessarily" soften the phrase.