While state TV reported Rajapaksa had cruised to a comfortable election win, Fonseka and his political allies were reported to be in a five-star hotel in the Sri Lankan capital, the ColomboPage reported.
Military spokesman Brig. Udaya Nanayakkara said the government does not plan to arrest Fonseka or any of his allies holed up in the hotel, the report said.
But the spokesman said those he described as army deserters staying with the general would be taken into custody.
The report said Fonseka and his allies had been talking of a possible government move to arrest them and contacted foreign news agencies to express their fears.
Both Fonseka and Rajapaksa had been credited with the Sri Lankan military's victory in May that ended the 26-year-old Tamil Tiger rebels' fight for a separate homeland for the Tamil-speaking Tamil minority in the largely Buddhist Sinhalese majority island nation. Fonseka and the Rajapaksa had a falling out in the post-war period, and Fonseka later became the opposition party's presidential candidate.
The BBC reported about 100 armed troops had surrounded Fonseka's hotel and quoted a government spokesman that they were looking for deserters but not Fonseka.