However, Congress, which had backed Independent candidate R K Anand who lost the poll, questioned the claim saying how could the MLAs do this when they had to deposit their own pens and mobile phones while entering the Assembly Secretariat for voting.
"This is a wild allegation levelled by INLD," party leader Kuldeep Sharma said.
"The pen theory is an allegation being imposed by the INLD," said another party leader Karan Singh Dalal.
Leader of Opposition in Haryana Assembly and INLD leader Abhay Singh Chautala blamed Congress for the defeat of INLD and Congress backed candidate Anand.
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"Congress party's 14 votes were rejected because they registered their votes with another pen other than the one provided by the Returning Officer to record their votes in the voting compartment," Chautala claimed.
Anand was defeated by BJP-backed media baron and Independent candidate Subhash Chandra.
The Haryana Assembly has 90 members. Out of 90 votes, Singh got 40, Anand 21 and Chandra got 15 votes while 14 votes were rejected.
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Addressing a press conference at his residence, senior Congress leader Dalal said his party has lodged a complaint with the Election Commission and the Vidhan Sabha Secretariat about the pen theory being floated to defame the party and its members.
"We demand an inquiry into this. Who is saying it was a sabotage by the Congress members, this is wild and totally baseless allegation being floated around," he said.
Notably, according to rules, during poll proceedings, voters should use only the pen provided by the Returning Officer to record their votes in the voting compartments.
Carrying of mobile phones etc is also not allowed inside the polling area.
Dalal said it was a pre-planned conspiracy of the INLD as well as the BJP to defame them.
"In fact, after Mr R K Anand praised Congress leadership including Sonia Gandhi, Rahul Gandhi and expressed his faith in our party's policies and programmes, this upset INLD leader Abhay Chautala since his party had earlier given backing to Anand's candidature. It is in fact, the INLD votes which are invalid and not ours, this is a conspiracy by the ruling BJP and its 'B' team INLD to defame us," he said.
"We did not make use of any unauthorised pen. Our mobile phones, like our pens, had already been deposited outside the polling area," Sharma said.