Opposition candidate Sarath Fonseka accused the government of pushing senior army commanders to appear on state-run television to express their public support for Rajapakse.
"By getting very senior officers to side with the president, the government is preparing the ground to hold on to power by using the army to suppress the people's will," Fonseka's spokesman Anura Kumara Dissanayake told reporters.
Rajapakse called Tuesday's vote two years ahead of schedule to benefit from the government's defeat of the separatist Tamil Tiger rebels after decades of ethnic warfare on the island.
But he faces a surprise rival to power in Fonseka, the former general who led the troops to victory in May.
The two fell out over who deserved credit for crushing the rebels, and allegations that Fonseka was himself planning a coup after being sidelined.
Military spokesman Udaya Nanayakkara denied that senior officers were being dragged into the election battle.