Sixty-eight lawmakers voted on Thursday to reject the proposed agenda for the extraordinary session, 36 voted against.
Speaker of the Seimas Loreta Graužinienė then announced a second vote on ending the extraordinary session and this time 67 MPs voted in favour and two abstained.
The extraordinary session lasted only for 12 minutes.
Opposition leader Andrius Kubilius, a conservative, said that the abrupt ending of the session was a stark violation of the constitutional rights of the opposition and that he would therefore refer the issue to the Constitutional Court.
"We will turn to the Constitutional Court, as we can see a very serious violation of the Constitution by this way of running Seimas meetings. Graužinienė's role will also deserve scrutiny, although the entire ruling majority is responsible and therefore we have to look into the issue of whether the ruling coalition, and its leader the prime minister, can continue to govern Lithuania according to constitutional principles," Kubilius said on Thursday.
Seimas Speaker Graužinienė, of the Labour Party, has retaliated by accusing the opposition of disrespecting the national anthem.
Opposition MPs stormed out of the room in protest, while the rest of the Seimas members were singing the anthem, a tradition of opening and closing Seimas sessions.
This, Graužinienė says, constitutes contempt for national symbols, an offence punishable by law.
"This is clear disrespect for the Lithuanian national anthem and such behaviour is unbecoming for elected members of parliament, possibly a violation of the law," Graužinienė said in a statement.
She added that she would review video footage from the meeting and might "turn to the Ethics and Procedure Commission over possible violation of law".
The Lithuanian parliament gathered on Thursday to continue the extraordinary session, following a decision of the parliamentary Commission on Ethics and Procedures that procedures were violated when the Seimas' concluded the sitting last week.
The Seimas' opposition collected 48 signatures to call an extraordinary parliamentary session last week, but the session's agenda was voted down by governing parties.
The opposition wanted to hold an extraordinary parliamentary session to launch an impeachment procedure against Labour MP Vytautas Gapšys who was sentenced in the party's fraudulent bookkeeping case.
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