Is that a correct sentence?

The registration number will be obtained after receiving the certificate.

It is unclear who will "obtain" the certificate, so I would chose another verb:
The registration number will be given out after receiving the certificate.（比较清楚)

The registration number will be given to you after receiving the certificate. (最清楚） 

Is that a correct sentence?

The registered number will be given after receiving the certificate.

Is that a correct sentence?

The registration number will be obtained after receiving the certificate.

It is correct. However, it would technically be more accurate to say, "You will obtain the registration number when you receive the certificate" or "The registration number will be obtained when you receive the certificate". It's hard to tell without the context of the statement.