Beijing stated its opposition to "any form of official exchanges with Taiwan, including military exchanges and cooperation", foreign ministry spokesman Geng Shuang told reporters, urging Singapore to "stick to the 'One China' principle".
Taiwan is a self-ruling democracy but Beijing still sees it as part of its territory. Relations have grown increasingly tense since the island's new China-sceptic president Tsai Ing-wen took power in May.
The shipment of Terrex Infantry Carrier Vehicles and other Singaporean military equipment has been held in Hong Kong since last Wednesday due to a "request for routine inspections" by customs, Singapore's defence ministry said.
Media reports in Hong Kong and Taiwan said the vehicles were on their way back from a training exercise in Taiwan.
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Singapore and Taiwan have a longstanding defence agreement signed in 1974, "Project Starlight", enabling Singaporean troops to train in Taiwan alongside Taipei's forces. The city-state sends up to 15,000 troops a year to the island.
But it has in recent years explored closer military ties with China, conducting a joint exercise in 2014.
Hong Kong is semi-autonomous after being handed back by Britain to China in 1997 and enjoys freedoms unseen on the mainland, but there are increasing fears over Beijing's interference.
"For quite some time, Singapore has been pretending to seek a balance between China and the US, yet has been taking Washington's side in reality," it said.
It accused the city-state of "hypocrisy" and threatened punitive measures that would "profoundly impact Singapore's economy".
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