The raids and detention of the Sunni minister's staff came hours after President Jalal Talabani, a Kurd who often mediated among the fractious Sunni, Shi'ite and Kurdish blocs, left for Germany after suffering a stroke that could end his moderating influence in Iraqi politics.
Finance Minister Rafie al-Esawi, a member of the Sunni-backed Iraqiya bloc, said more than 100 of his bodyguards and staff were snatched illegally by militias on Thursday.
He blamed Mr Maliki for orchestrating the raids to target opponents. The prime minister's office said only six bodyguards were arrested under counter-terrorism laws.
Politicians and authorities gave conflicting accounts of the incident, but it was reminiscent of a year ago when Iraqi authorities sought the arrest of Sunni Vice President Tareq al-Hashemi and his bodyguards, accusing them of running death squads.
Last year's Hashemi case plunged the fragile power-sharing deal among Shi'ite and Sunni Muslims and Kurds into turmoil, with Sunni politicians boycotting parliament.
Mr Hashemi later fled to Turkey and was sentenced to death in absentia.
"This confirms there is continued systematic targeting of the Sunni symbols and leaders participating in the political process," Sunni leaders said in a statement.
Violence in Iraq is down from the days of intercommunal slaughter that erupted soon after the 2003 US-led invasion that toppled Sunni dictator Saddam Hussein.
But many Sunni leaders feel they have been sidelined from power-sharing by Mr Maliki as he consolidates his authority under a constitution that grants the premier wide powers.