The Muslim Brotherhood said on its web site that parliament speaker Fathi Sorour had expelled Mustafa Mohamed Mustafa on Saturday "to deny the Muslim Brotherhood MPs the chance to reveal new scandals of the Egyptian government in the matter of the French ship Clemenceau".
The Clemenceau is a 27,000-tonne aircraft carrier which is heading to India to be scrapped.
Environment group Greenpeace says the ship contains hundreds of tonnes of hazardous materials, including 500 tonnes of asbestos.
The government this week allowed the Clemenceau through the Suez Canal en route to India and said the ship did not pose an environmental threat.
The Muslim Brotherhood is Egypt's main opposition group and its members won nearly a fifth of the seats in parliament in elections last year - their biggest ever bloc.
The ruling National Democratic Party won most of the remaining seats, leaving it in control of the chamber.
The ship contains hazardous
materials, says Greenpeace
Egypt's state MENA news agency said Sorour expelled Mustafa "because of his insistence on speaking in a loud voice and his criticism of the government for allowing the ... Clemenceau to pass through the Suez Canal without consulting parliament".
Sorour said "the chamber's decision (to expel Mustafa) was to preserve order in the chamber and was not directed at the person of the honourable deputy", MENA reported.
Brotherhood lawmaker Hussein Mohammed Ibrahim said the expulsion "reflected clear obstinacy from the parliament and the ruling party against the Brotherhood", the web site said.
The Brotherhood lawmakers returned to the chamber after Mustafa handed Sorour a written apology and was allowed back.
The Brotherhood, founded in 1928, sidesteps an official ban on its existence by fielding candidates as independents for parliament.