Japan is holding back more than £34m in Unesco funding following a protest against the listing of documents related to the Nanjing massacre.

The foreign minister, Fumio Kishida, confirmed Japan had suspended this year’s contribution, totalling 4.4bn yen (£34.4m), but denied any direct link to an incident that still hangs over frosty diplomatic relations between Tokyo and Beijing.

Japan – one of Unesco’s biggest funders – warned last year that it might pull the funding after the UN cultural and scientific body agreed to Beijing’s request to register disputed Chinese documents recording the mass murder and rape committed by Japanese troops after the fall of the Chinese city of Nanjing 1937.

The documents were inscribed in the UN body’s Memory of the World list.

The massacre is an exceptionally sensitive issue in the often tense relations between Japan and China, with Beijing charging that Tokyo has failed to atone for the atrocity.

Tokyo had called for the Nanjing documents not to be included and accused Unesco of being politicised.

The Japanese military invaded China in the 1930s and the two countries fought a full-scale war from 1937 until Japan’s defeat in the second world war in 1945.

China says 300,000 people died in a six-week spree of killing, rape and destruction after the Japanese military entered Nanjing.

Some foreign academics put the number lower but there is very little mainstream scholarship doubting that a massacre took place.

Japan’s official position is that “the killing of a large number of noncombatants, looting and other acts occurred”, though adds “it is difficult to determine” the correct number of victims.

However, some conservatives and nationalists deny that atrocities were committed, a source of regular regional friction.

Beijing has rejected Japan’s protest over the Unesco decision.

Some civic groups are attempting to have thousands of documents linked to Japan’s controversial wartime brothels entered into the UN registry.

Tokyo frequently clashes with its Asian neighbours over its war record, with many accusing the country of failing to atone for atrocities or recognise the suffering that took place under Japanese militarism.

The Memory of the World register, set up in 1992, is aimed at preserving humanity’s documentary heritage, and currently holds 348 documents and archives that come from countries all over the world.