The Turnbull government has suffered a second embarrassing failure in Parliament, effectively voting to call on itself to explain its own failures on multinational tax avoidance.

Labor said the mistake is unprecedented in the federal Parliament, the first time a second reading amendment has passed the House of Representatives and leaving uncertainty about how the government could unwind its position.

Manager of Opposition Business Tony Burke blamed Financial Services Minister Kelly O'Dwyer, who he claimed had forgotten to vote against the amendment on behalf of the government, meaning it passed unanimously.

The amendment, moved by shadow assistant treasurer Andrew Leigh, called on the government "to explain why it has failed to close tax loopholes and increase transparency in Australia".