At the time, everyone thought that Sirius betrayed James, and murdered Pettigrew and several muggles. Lupin would have believed that he alone knew that Sirius was an animagus.
What reasons might he have had for withholding this information from the Ministry or Dumbledore? Lingering doubts/loyalty? Fear of persecution by association?
I forgot about this part:
He didn’t want to admit that he had betrayed Dumbludore’s trust.