"I have been informed of the operations which took place overnight against oil sites. We must continue with this logic," Jean-Yves Le Drian said during a New Year trip to the base, where around 250 French personnel are deployed.
The first French strikes of 2016 were carried out by two Mirage 2000s around 2:00 am, according to a military source on the base.
France is a key member of the US-led coalition that is carrying out air strikes on IS positions in Iraq and Syria.
The aerial campaign was stepped up after the deadly attacks claimed by IS in Paris in November last year.
Bombing raids have increasingly focused on IS's oil infrastructure, which provides a key part of the jihadists' funding.
Two other jets took off from the Jordanian base Friday morning to serve as aerial support for Kurdish peshmerga forces battling IS around Sinjar, the northern Iraqi town that was cleared of the jihadists in November, the military source said.
They returned after five hours to accompany Le Drian's plane as it landed in Jordan, the source added.
The name of the base, where six Mirage fighter jets are stationed, is not being disclosed at the request of authorities in Amman.
Other French military assets in the region include the Charles de Gaulle aircraft carrier, currently stationed in the Gulf, and six Rafale jets in the United Arab Emirates.
France carried out more than 390 strikes against IS during 710 missions last year.
It has provided extensive air cover for Kurdish and Iraqi forces battling the extremists in Iraq and has flown sorties over Syria since September, according to the military.