President Rajapaksa had campaigned for the polls held yesterday for the Western and Southern Provincial Councils, both in the ethnic majority Sinhalese heartland, which account for more than a third of the country's electorate.
The ruling United People's Freedom Alliance (UPFA) won 33 of the 55 seats in the southern province, down from 38 in the 2009 poll, with three opposition parties winning the rest, final results from the election office showed.
The ruling party's vote dropped from 66.91 in 2009 to 57.42 per cent in the district, one of three that make up the southern province.
In the West, the UPFA suffered a loss of 12 seats in the 104-member council compared to the 2009 poll when it won 68 seats.
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The main opposition United National Party (UNP) won 28 seats, a loss of two.
The party pushed the third force JVP to fourth place in the West. JVP won six seats up from three in 2009.
Fonseka's party ended up having 12 seats in the two councils as they won three seats in the South.
The main opposition UNP retained its 14 seats while suffering a loss of two seats in the west.
President Rajapaksa had based his campaign on the issue of the Sri Lanka resolution adopted on Thursday at the UN Human Rights Council (UNHRC).
The UNHRC resolution prescribed an international investigation into alleged war crimes committed by government troops in the final battle with the LTTE five years ago.
The opposition urged voters to issue a warning to the Rajapaksa's government for bungling of the economy, his inability to uphold the rule of law, curb corruption and drug pedalling.
The government banked on its unprecedented infrastructure development with ports, airports and highways.