Chief Justice Abdulla Saeed and another judge, Ali Hameed, were arrested hours after the government declared a state of emergency.
No details were given about the investigation or any charges.
The turmoil began when President Abdulla Yameen refused to obey a court order to release political dissidents.
The opposition have called the government moves a "purge" and there has been international condemnation.
Maldives is a nation is made up of 26 coral atolls and 1,192 individual islands, and tourism is a vital part of its economy.