China said Wednesday a flight by 16 military aircraft over hotly contested waters off Malaysia was routine training, after the Southeast Asian nation accused Beijing of breaching its sovereignty. 

Malaysia scrambled fighter jets Monday to intercept the Chinese air force transport planes that appeared off Borneo over the South China Sea, where it has overlapping territorial claims with Beijing.

The Malaysian foreign minister criticised the flight as an "intrusion" and said the government would lodge a protest with Beijing and summon the Chinese ambassador. 

But a spokesman for the Chinese embassy in Kuala Lumpur said the "activities are routine flight training of the Chinese air force and do not target any country".

"According to relevant international law, Chinese military aircraft enjoy the freedom of overflight in the relevant airspace," he said.

The planes had not entered any other country's territorial airspace, the spokesman added in a statement.

The aircraft came within 60 nautical miles (110 kilometres) of the Malaysian part of Borneo, and did not respond to attempts to contact them, prompting Malaysia to scramble jets, according to the country's air force.

They turned back before entering Malaysian airspace over its territorial waters.

But Foreign Minister Hishammuddin Hussein said they had entered the country's "maritime zone" -- an area that extends much further from the coast -- and described the incident as a "breach of the Malaysian airspace and sovereignty".

China has laid claim to nearly all of the South China Sea and has built numerous military outposts on small islands and atolls, angering other countries with competing claims to the waters.

Malaysia-China relations are usually warm but Monday's incident comes after a build-up in tensions over the sea, which is home to key shipping lanes and is believed to harbour rich oil and gas deposits.

Last year, a Chinese survey ship had a long stand-off with a Malaysian oil exploration vessel off Borneo.

Other claimants in the sea include Vietnam, the Philippines, Brunei and Taiwan.

The United States has also sent warships through the waters to assert international rights to freedom of navigation, angering China.