How was Sirius Black still a largely unknown Animagus at the time of Prisoner of Azkaban?

Question

We know that Peter Petigrew told Voldemort about Sirius being an Animagus from the following question:

How did Lucius Malfoy know Sirius's Animagus form?

However this would have happened at some point after POA and Order of the Phenonix with some high ranking Death Eaters still having considerable power at the ministry such as Lucius Malfoy.

My question is how did the ministry of magic not know Black was an Animagus ?

I presume they were still hunting him because it's only later that they admitted he was innocent.

What made the Ministry admit Sirius was innocent?

Also we know the at the start of POA Both Remus Lupin and Severus Snape believe Sirius to be guilty of thirteen murders at this stage so how was this information not known at the ministry ?

Answer 1

Because Lupin (and the Marauders) didn't tell anyone about Sirius being an Animagus

Not even Dumbledore.

“Last night Sirius told me all about how they became Animagi,” said Dumbledore, smiling. “An extraordinary achievement — not least, keeping it quiet from me.”

Neither did they register themselves as Animagi.

“I sometimes felt guilty about betraying Dumbledore’s trust, of course he had admitted me to Hogwarts when no other Headmaster would have done so, and he had no idea I was breaking the rules he had set down for my own and others’ safety. He never knew I had led three fellow students into becoming Animagi illegally.”

Therefore, it can easily be said that the Ministry had no idea Sirius Black was an Animagus. If you aren't on the records, you aren't an Animagus.

“Because . . . because people would know if Peter Pettigrew had been an Animagus. We did Animagi in class with Professor McGonagall. And I looked them up when I did my homework — the Ministry of Magic keeps tabs on witches and wizards who can become animals; there’s a register showing what animal they become, and their markings and things . . . and I went and looked Professor McGonagall up on the register, and there have been only seven Animagi this century, and Pettigrew’s name wasn’t on the list —”

So the Ministry can be searching for Sirius Black all they want, but if he's in his Animagus form, no one would be able to recognise him or his markings -- simply because he isn't registered.

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This brings us back to the question: Why did Lupin keep his mouth shut?

3 reasons:

1. He was "too cowardly"

   “But I didn’t do it. Why? Because I was too cowardly.”

2. He felt bad for betraying Dumbledore's trust

   “It would have meant admitting that I’d betrayed his trust while I was at school, admitting that I’d led others along with me and Dumbledore’s trust has meant everything to me. He let me into Hogwarts as a boy, and he gave me a job, when I have been shunned all my adult life, unable to find paid work because of what I am.”

3. He chose to believe that Sirius was using Dark Magic

   “And so I convinced myself that Sirius was getting into the school using Dark Arts he learnt from Voldemort, that being an Animagus had nothing to do with it ...so, in a way, Snape’s been right about me all along.”

Trust is an important factor here. If Remus had spilled the beans on the Marauders to Dumbledore, it would've been known that he had kept this secret quiet for much over a decade. He believed that he would have been fired as a teacher if he had told Dumbledore about his 3 illegal Animagi friends.

Not only that, he was in denial that Sirius used his Animagi abilities to escape Azkaban: to kill more people, Harry included. And who's fault is that in the first place? Remus Lupin; the guy who "indirectly" made them become Animagi. Whatever wrongs Sirius would have done after escaping Azkaban would be all Lupin's fault, as he believed (wrongly, of course).

Answer 2

He was unregistered

The Ministry doesn't know about every Animagus in Britain. Every Animagus is required by law to sign up to a public register declaring their existence as an Animagus, as well as the animal they turn into and any of their distinguishing markings. Minerva McGonagall was a registered Animagus.

We know of 4 unregistered Animagi:

James Potter, Peter Prettigrew, Sirius Black - All perfected the art at the age of 15, to help Remus Lupin, a werewolf, during nights of a full moon, and keep him in check.

Rita Skeeter - Deliberately didn't register because it helped her journalism career.

The Ministry never found out how Sirius escaped Azkaban, and he never registered himself, so they had no idea he was an Animagus.

Answer 3

As for the actual question as to why Lucius Malfoy or one of the other fine upstanding Death Eaters didn't tell the Ministry, there was a good reason and a very good reason.

A Good Reason

Lucius always played things close to the vest. He knows knowledge is power, and just giving away secrets gets you nowhere. If he had told the Ministry, they would have tried to track down and arrest Sirius. And that's assuming one of Dumbledore's cronies in the Ministry, like Weasley, didn't pass the information on.

If they keep it to themselves, they can follow Sirius around. He might lead them to other Order members, or safe houses. Even if he can't lead them to #12, if they see him in the neighborhood enough, they will know to keep an eye on the Square. Or just firebomb it.

Of course this was all spoiled because Snape was a dirty double agent, but the Death Eaters didn't know that.

A Very Good Reason

It would be very difficult to pass the information to the Ministry without incriminating himself. Lucius obviously can't reveal that the information came from Wormtail, the supposedly dead man Dumbledore claims is a Death Eater and the reason Sirius was imprisoned. So what can he do?

Lie and say he has some sort of super Time Turner and went back to observe things? Unbelievable and illegal.

Claim he just remembered seeing Sirius transform when he was Imperiused to work for the Death Eaters? He looks stupid, incompetent, and suspicious.

Claim he just saw a dog on the street transform into Sirius (or verse vica)? He'll have to explain where and when, and why he let Black escape.

So yes, Malfoy knew. But no, he could not and would not tell the Ministry.