Joint Opposition media spokesman Mangala Samaraweera accused Army Commander Daya Ratnayake of deploying troops to campaign for Rajapaksa, also the Commander-in-Chief of the army.
Samaraweera said Ratnayake's conduct was in violation of election laws and will be reported to the international observers.
"The deployment of soldiers for such political work is destroying the dignity of the (men in) uniform," he said.
Samaraweera claimed the military had last month included Rajapaksa's election propaganda leaflets in soldiers' pay packets.
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"The statement that the Army has employed soldiers for election related propaganda is baseless and extremely presumptuous", said military spokesman Brigadier Ruwan Wanigasooriya.
The Opposition and election-monitoring groups have accused the ruling Sri Lanka Freedom Party of abusing state resources for Rajapaksa's campaign.
The SLFP has in turn accused the monitoring groups of bias.
Rajapaksa faces his former health minister Maithripala Sirisena, who defected to the opposition to become the common candidate of the opposition for the January 8 presidential election.
Sirisena led a revolt in Rajapaksa's ruling coalition, taking 11 ministers and lawmakers along with him.