Mr Baker said passengers deserved a more comfortable time
Airlines which fail to get at least 95% of passengers through check-in within 15 minutes should be fined, the Liberal Democrats have said.
Transport spokesman Norman Baker said queues had to be minimised at Gatwick and Heathrow to ensure a "smooth and efficient journey".
Delays should also not hold up planes on runways or leave them circling over cities, raising emissions, he added.
Passenger experience had to be "higher up the industry's agenda", he said.
A report by Mr Baker, MP for Lewes, says: "Any travellers caught up in the chaos at the opening of Terminal 5 will recognise claims by the head of the International Air Transport Association, Giovanni Bisignani, that Heathrow is a 'national embarrassment'.
"London First has condemned the 'hassle factor' of the delays and poor customer service at Heathrow."
Mr Baker said current standards meant there were fines for delays at security queues and those caused by a lack of available luggage carousels.
But he added that no penalty existed for excessive queues at check-ins run by airlines.
Those failing to deal with at least 95% of passengers within 15 minutes should be fined by the Civil Aviation Authority, Mr Baker said.
His report adds: "Air passengers deserve a smooth and efficient journey from arrival to when they land at their destination.
"Queues at check-in and security should be minimised and passenger comfort, not retail takings, should be put first and foremost while waiting for flights.
"Delays should not hold up planes for long periods of time on the runway, nor should flights be left stacking over cities, wasting time and creating significantly increased carbon emissions. Unfortunately this is not the case at present."
Mr Baker's report also calls for the carbon emissions details of passengers' journeys to be printed on tickets.