Labour leader David Shearer has called this inconsistent, because Dotcom passed a character test to gain residency.
But Mr Key said the two tests were "slightly different".
When considering character for residency, immigration officials look at an individual's record, including whether the applicant's convictions have been wiped away under clean slate provisions.
For overseas investment, officials look at a person's history, including convictions, and disregard any clean slate provisions.
Dotcom, who was denied bail today (Wed) following his arrest on Friday in an FBI-led raid, said at the time it did not make sense to grant him residency but not allow him to buy the home he wanted for his family.
Mr Key said immigration officials had reviewed Dotcom's case and were satisfied that correct procedure was followed and the law was properly applied.
But officials will look at whether the potential anomaly should be corrected.
Mr Key repeated that he did not think criminal convictions should, by themselves, necessarily disqualify an applicant for residency.
"It's not unusual for someone who has a criminal record to be granted residency. It happens every day."
Dotcom effectively had a clean record because of Germany's clean slate provisions, he said.
Jonathan Coleman, who was Immigration Minister at the time Dotcom's residency was granted, was informed of the decision to grant residency as it was being made - effectively giving him an opportunity to object, which he did not.
Mr Key said he had no issue with the minister's handling of the case.
