William Amos said the incident occurred on Wednesday while he was "attending House of Commons proceedings virtually in a non-public setting."
Amos is a federal Member of Parliament (MP) for Pontiac, Quebec for Canada's governing Liberal party.
"I urinated without realizing I was on camera," he said in a statement posted on Twitter, adding that he was "deeply embarrassed" by his actions.
"While accidental and not visible to the public, this was completely unacceptable, and I apologize unreservedly," Amos said.
This is the politician's second on-camera embarrassment in a matter of weeks.
On April 14, he was spotted in a state of undress during a parliamentary video call. A screenshot from the call circulated widely online.
Fellow MP Claude DeBellefeuille, of the Bloc Québécois party, pointed out Amos' appearance at the time.
"We have seen a member during question period improperly dressed. That is, unclothed. So perhaps remind the members, especially the male members, that suits and ties are appropriate," said DeBellefeuille in French, according to the parliamentary translator.
Amos apologized at the time and called the April incident a "a really unfortunate mistake" that occurred as he changed into work clothes after a jog.
Wednesday's incident prompted him to go further. Amos is a lawmaker who also serves as parliamentary secretary to Canada's minister of innovation, science and industry.
"I will be stepping aside temporarily from my role as Parliamentary Secretary and from my committee duties so that I can seek assistance," Amos said.
He added that he would continue to serve as an MP.
The politician was previously an environmental lawyer and was first elected as an MP for Pontiac in 2015.