Congress on Monday suffered a setback losing two out of three seats it had contested in the biennial elections to Maharashtra legislative council, which it fought in alliance with the Sharad Pawar-led NCP.

Congress could retain only the Latur local bodies seat in which Dilip Deshmukh, younger brother of union minister Vilasrao Deshmukh, was re-elected for the third time, while lost Chandrapur and Amravati local bodies seats in the polls held on May 25 for six seats.

While retaining Amravati seat, BJP defeated congress nominee Rahul Pugalia to claim Chandrapur seat which was earlier held by an independent.

On the other hand, congress's alliance partner NCP retained Raigad seat and also won Parbhani which was though held by congress was allotted to NCP in the pre-poll understanding reached between the two parties.

While, counting for the Nashik local bodies was in progress, the state electoral office said.

Meanwhile, congress sources said that they lost the Amravati seat by a margin of 10 votes.

"Ajay Navandar, the independent candidate had sought party ticket and was backed by local congress MLAs in Amravati. However, the party leadership refused to nominate him and instead fielded Aniruddha Deshmukh, the district unit party chief," they said, adding that Deshmukh could have not been supported by the NCP due to differences at the district level.

According to sources, Congress did not have the requisite numbers in its favour to claim Chandrapur seat.