The service was also hit by a brief power cut in the morning rush hour, prompting television footage of passengers walking through the tunnel next to a stationary train.
Prime Minister Tayyip Erdogan opened the multi-billion dollar Marmaray, a 13 km (8-mile) tunnel, to great fanfare on Tuesday. It is expected eventually to carry some 1.5 million passengers a day under one of the world's busiest waterways.
State rail company TCDD said the service was facing strong demand. It had closed one of its stations to alleviate overcrowding. Some passengers riding the trains for the first time and unfamiliar with the systems had pressed 'emergency stop' buttons, causing delays.
"We expect our passengers to take into account the crowds and to avoid constantly going back and forward if possible to make space for other passengers," it said.
The two bridges and ferry services crossing the Bosphorus are heavily crowded with commuters in Europe's biggest city.
Government critics say the opening of the tunnel, one of Erdogan's "mega projects" designed to change the face of Turkey, was rushed to coincide with Tuesday's 90th anniversary of the founding of the modern Turkish republic.
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Great peoples great achievments.
Great peoples great achievments.
This is a pretty amazing project. They already have two bridges linking Turkey to Europe across the Bosphorus strait. But those bridges are overcrowded so they built this tunnel. Worth reading about:
http://en.wikipedia.org/wiki/Marmaray