The request was read on the Senate floor on Tuesday morning.
The emergency rule was first introduced in the three states in May last year, before it was extended by another six months in November. A further extension will ensure it continues to November, three months to the general elections in Nigeria.
Mr. Jonathan had hinted during his last Presidential Media Chat on May 4 that the emergency rule would be extended.
He said the emergency rule was necessary for soldiers to effectively tackle the insurgency in the region.
Adamawa, Borno, and Yobe are three of the state most affected by the Boko Haram insurgency.
Critics of the emergency rule have stated that it has not reduced or stopped the killings by the Boko Haram insurgent group in the state.
At least two thousand people have been killed in Boko Haram related violence in the three states in 2014 alone.
The extension of the emergency rule would have to be approved by both chambers of the National Assembly to be considered legal.
