The opposition Congress retained the two Assembly seats - Kolaras (Shivpuri district) and Mungaoli (Ashoknagar district) - where bypolls were held on February 24, but with a reduced margin.
"We fought to win but a bit was left in our effort," he told reporters at his residence here when asked to comment on the bypolls' outcome.
"We are pained we could not win the by-elections," said Chouhan, who along with some senior members of his Cabinet took part in the campaigning.
"The Congress won Mungaoli by 22,000 votes in 2013. This time we lost to the Congress by around 2,100 votes."
The chief minister expressed confidence that his party would win the Assembly polls, slated for later this year, with a comfortable majority.
The BJP is ruling Madhya Pradesh since 2003.