The Cabinet decided that the ministers who have failed to attend sessions are no longer "allowed to manage ministries.
Iraq's Shiite-dominated Cabinet suspended boycotting Sunni-backed ministers Tuesday.
The measure targeted Sunni-backed Iraqiya, which has sought to boycott parliament and the cabinet since Shi'ite Prime Minister Nuri al-Maliki ordered the arrest of the country's Sunni vice-president, heightening fears of an upsurge in sectarian violence after last month's withdrawal of U.S. forces.
Tuesday's ruling by the rest of the cabinet bars three protesting Iraqiya members, namely Finance Minister Rafie al-Esawi, the science minister and the education minister, from running their offices, a spokesman for the government said.
"Absent ministers will not be allowed to sign any orders or run their ministries until they stop boycotting cabinet sessions. Then everything will return to normal and they can resume running ministries," Ali al-Moussawi, Maliki's media adviser, told Reuters.
The political crisis is the worst since the power-sharing government was formed a year ago following an inconclusive 2010 election. It divided posts in government and the presidency among Shi'ite and Sunni Muslims and ethnic Kurds.
Maliki's government moved to arrest Sunni Vice President Tareq al-Hashemi on Dec. 19 on charges he ran a death squad. It also sought to sideline a Sunni deputy prime minister after he branded Maliki a dictator.
Hashemi denies the charges and sought refuge in the autonomous Kurdish region where he is unlikely to be arrested.
Iraqiya lawmakers have boycotted the parliament and several Iraqiya cabinet ministers have stayed away from government meetings in protest. However, some others have attended, underscoring splits in the Sunni-backed bloc.
Political blocs this week began talks on trying to organise a national conference to resolve their differences. But already the turmoil is fueling fears in the Sunni minority that Maliki is seeking to shore up Shi'ite power and sideline Iraqiya.