His comments came days before the country's 6 November parliamentary elections.
Aliyev said that an alleged coup plot was uncovered two weeks ago that would have thrown Azerbaijan into civil war and anarchy if the conspirators had had their way.
He said that Azerbaijan had faced a serious threat but had dealt with it "categorically, bravely and according to law." He told the ministers that should be a "lesson" to them all.
He accused the alleged plotters of conspiring with exiled opposition leader Rasul Quliyev whom he described as a leader of the "international mafia." Aliyev also accused Quliyev of being involved with international organized crime.
"Where is [opposition leader] Rasul Quliyev? A thief and a mafioso, why is he not coming to Azerbaijan? Let him come and answer our questions. Is he afraid? And others will be scared too, because they don't have enough courage," Aliyev said.
Today, nearly 10,000 supporters of the ruling New Azerbaijan party rallied in a Baku square, many reportedly waving portraits of Aliyev and his late father, Heydar, the previous president.
RFE/RL's complete coverage of the November 6, 2005, legislative elections in Azerbaijan and their aftermath.
Timeline: How The Elections Have Unfolded
A photo gallery of the Azerbaijan opposition protests in Baku on November 9, 2005.