"It is not fair to make comparisons with the provincial election of 2009. That was the time when the government had defeated the LTTE. But now the conditions have changed," senior minister Maithripala Sirisena told reporters.
He said the comparisons made by analysts for the loss were unreal.
Compared to the 2009 election, the United People's Freedom Alliance's vote share in the Western and Southern provincial council polls held on Saturday dropped from high 60s in percentage to mid 50 per cent points.
However, the coalition still won the two councils.
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The election was held as a test of popularity for President Rajapaksa as he based his campaign on urging the public for a stronger mandate against what he termed anti-Sri Lanka action by the West to undermine the country through the third successive resolution at the UN Human Rights Council.
The resolution came to be adopted with 23 countries supporting the US move for an international investigation.
Most significantly for Sri Lanka, India was one of the 12 nations that abstained from voting.
The government retained the control of the two provinces with reduced numbers of seats as the opposition made significant gains.
It was the first time the government had suffered a loss of its vote or the opposition had gained votes in the two provinces since President Rajapaksa's military campaign ended the LTTE's nearly 30-year campaign to set up a separate Tamil homeland.
President Rajapaksa has been holding staggered elections at provincial level to capitalise on his popularity among the majority Sinhalese for ending the Tamil separatist campaign.