A court last week ordered two months of pretrial detention for Adnan Hadzhizade and Emin Milli, who were charged with hooliganism after what authorities called a fight with several men in a Baku cafe.
Police let the other men - who Hadzhizade and Milli said were the attackers - go free.
President Ilham Aliev has faced persistent criticism over the heavy-handed treatment of independent media and opposition parties in the oil-rich former Soviet republic.
Hadzhizade is a video blogger and member of the "OL!" movement, one of several opposition groups in the country, as well as an employee of British oil giant BP, which has major investments in Azerbaijan's massive oil and gas industry. Milli is an opposition youth activist who also runs an Internet TV program.
The U.S. Embassy voiced concern about their detention, as did Germany, saying the two men were denied access to lawyers and medical care and that the pretrial detention court order was excessive. The case also prompted criticism from international journalism advocates.
On Tuesday, Azerbaijan's Interior Ministry and Prosecutor General's office denied those accusations and accused the embassies and foreign-funded rights groups of meddling in the country's internal affairs.
"We call on the diplomatic missions of certain countries in Azerbaijan to stop interference in the investigation process and in the internal affairs of (Azerbaijan), which goes beyond the framework of their missions," it said.