Indonesia's biggest low-cost airline was left scrambling Friday after a second day of major delays saw thousands of angry passengers barricading gates and staging noisy protests inside the country's main airport terminal.

Lion Air has grounded 16 flights across the country since Thursday, stranding 6,000 passengers at the start of a traditional long weekend period to mark Chinese New Year, with the delays apparently caused by a combination of mechanical problems and the high number of travellers.

Annoyance boiled over into anger at Soekarno-Hatta International Airport, the country's main hub on Jakarta's outskirts and the epicentre of the transport chaos.

Transport ministry official Hadi Mustofa Djuraid said the problem spread from Lion Air until large parts of the terminal were in gridlock.

"They (passengers) blocked the gates of other airlines, causing a number of delays," he told AFP.

AirAsia announced Friday afternoon it had moved the boarding area for its passengers to another terminal to avoid the throngs demanding answers over the Lion Air situation.

Lion Air said the delays – triggered after three of its fleet encountered mechanical problems – were exacerbated by the massive crowds travelling for the peak holiday season.

"This is a domino effect," airline spokeswoman Adhitya Simanjuntak told AFP. "If the first flight was delayed, it continued to the next flight, and so it went on."

The delays spread throughout the entire network Friday, with passengers also left waiting at major terminals in Surabaya, Bali and Medan.

Lion Air – the country's most popular low-cost carrier – is already feeling the heat from above, with Transport Minister Ignasius Jonan refusing to consider the airline's requests for new flight routes until it cleans up its act.

"As a big company, Lion Air has performed very badly," said the ministry official, Djuraid. "It has no procedure for properly handling a crisis."

Lion Group, the airline's parent company, has in recent years struck two of the world's largest plane orders, worth US$46 billion.

Passenger air transport has been growing at an average of 20 per cent or more per year in Indonesia, with low-cost carriers in high demand across the archipelago nation of more than 17,500 islands.