A day after being prevented from entering Adzhara, Saakashvili told reporters on Monday "the restrictions we have imposed are very temporary".
Many key institutions in Adzhara, including security forces, customs officials and the Batumi port, are not under central government control.
Speaking in the capital Tblisi, the president said Georgia intended to respect trade contracts and would seek other outlets for cargo.
"We are taking part of the shipments to other ports, to the seaport of Poti. We are taking part of the land shipments to other checkpoints with Turkey and we are checking every cargo and this will last until the local government clarifies that the (28 March) parliamentary elections will be free and fair."
Batumi, about 20km from the Turkish border, has a 200,000 barrel-per-day oil terminal and handles oil and oil products from Kazakhstan and Turkmenistan for delivery to Mediterranean markets.
The owners of the oil terminal said earlier on Monday that loading was stable despite threats to block railways to the port.
"We have implemented all measures necessary to introduce control in the port, on the border checkpoint with Turkey, on the railways, and airspace," Saakashvili said.
The crisis flared early on Sunday after armed men loyal to Adzhara's leader, Aslan Abashidze, blocked Saakashvili and his entourage from driving into the region, and fired automatic rounds into the air over his motorcade.
Georgia is strategically important
to both Russia and the West
Saakashvili turned around and drove to the nearby city of Poti, where he convened an emergency cabinet meeting, ordered the military onto high alert, and ordered Adzhara's airspace shut down.
He then gave Abashidze until the evening to recognise Tbilisi's authority.
However, Russia - which has a military base inside Adzhara - has warned the Georgian authorities of "grave and unpredictable consequences" if they send their forces into the region.
Relations between Tbilisi and Adzhara have been tense for years.
Abashidze runs the region like a personal fiefdom, has withheld taxes from the central government and has set up his own security force which takes orders only from him.
The crisis over Adzhara is being watched closely in western capitals - not least because Georgia is on the route of a strategic pipeline which will soon start exporting crude oil from the Caspian Sea to world markets.
Georgia's separatist regions of Abkhazia and South Ossetia broke away from Tbilisi shortly after the Soviet Union fell apart in 1991.