China and the US are set for renewed confrontation after Beijing warned of serious repercussions following Washington's announcement of a $6.4bn (£4bn) arms deal with Taiwan.

Sanctions were imposed on US companies involved in the deal, and in one of a flurry of unsually strong statements condemning the American decision the Foreign Ministry said: "It will be un­avoidable that co-operation between China and the United States over important international and regional issues will also be affected." Earlier it had summoned US ambassador Jon Huntsman.

The Foreign Ministry statement will add to concerns about the knock-on effects of the deal, and whether it will hinder the prospect of new sanctions against Iran at the United Nations Security Council. Despite China's reluctance to act against its ally, the US was hopeful that it could win its backing if Russia was on board. Beijing will postpone high-level consultation on strategic security, arms control and non-proliferation issues, it said. The Defence Ministry said it was suspending military exchanges because of the "harm and odious effect" of the deal.

The dispute comes amid growing tensions over issues including trade, climate change and internet censorship.

"This is the strongest reaction we have seen in recent years," said Stephanie Kleine-Ahlbrandt, North East Asia project director of the International Crisis Group. But she added: "Our real sense is that China is looking to see what reaction it will receive from Barack Obama."

US officials made no immediate response to the Chinese reaction, which seemed stronger than expected.

The arms deal includes Patriot missiles, Black Hawk helicopters and minehunter ships. But, in an indication of US concern about Beijing's reaction, it does not include F16 fighter jets or a design plan for diesel submarines – both long sought by Taiwan.

Taiwan has been self-ruled since 1949, but Beijing continues to assert sovereignty over it and has said it is prepared to use military action if the island seeks formal independence. While the US does not technically have diplomatic relations with Taipei, it is legally obliged to ensure that Taiwan can defend itself and has long supplied it with arms.

Taiwan's Defence Ministry said the deal "gives us greater confidence in pushing for an amicable outcome in our relations with China, and will help promote peace in the Taiwan Strait".

China is believed to have more than 1,000 missiles aimed at the island. Taiwan's relations with the mainland have improved since President Ma Ying-jeou took office in 2008. But Beijing's reaction to the long-expected sale suggests it may have hoped the thaw would reduce US military cooperation. China's Taiwan affairs office said the deal "fanned the flames of Taiwan independence" and sent the wrong message, according to the Xinhua state news agency.

Washington and Beijing had boasted of a strengthening of bilateral ties, but in recent weeks the relationship has come under growing strain.

China is thought to be concerned that Obama faces growing domestic pressure to take a tougher line towards Beijing, and was angered by Hillary Clinton's speech on internet freedom last week. Although China warned that the speech could damage bilateral relations, both sides subsequently sought to play down the disagreement. Obama's national security adviser, Jim Jones, said in a speech on Friday that the US was "bent toward a new relationship with China as a rising power in the world".

But Jin Canrong, a professor of international studies at Renmin University, said the arms sale would give Beijing a "fair and proper reason" to accelerate weapons testing.