A senior Belgian intelligence officer is under investigation over allegedly sharing secrets with the Russians, in a case that exposes fears about spying in the European Union and Nato.

An unnamed major who is the head of division at the general intelligence and security service (GISS), the equivalent of M16, is accused of having exchanged confidential information with a Serbian woman believed to be a Russian agent.

In another blow to the agency, it emerged that Clement Vandenborre, the head of counter-intelligence at GISS, was suspended from his post at the end of last month. He is alleged to have shredded confidential documents, according to the Flemish daily De Morgen, which broke the story on Vandenborre and the Russian spying allegations.

A spokesperson for Belgium’s defence ministry confirmed that an investigation was under way. “In order not to hinder this investigation, we will not comment on this subject,” the spokesperson said.

Die Welt reported earlier this week that, according to a confidential assessment prepared by the EU’s foreign affairs service, about 250 Chinese and 200 Russian spies were working in the Belgian capital, which is also home to Nato headquarters.

The latest allegations against the GISS will deepen long-standing concerns about infighting, low morale and rogue missions in the feuding organisations that make up Belgian intelligence.

The Dutch-language public broadcaster VRT reported this week that two senior officers from Belgium’s intelligence service had travelled to Damascus in 2016 to negotiate with the regime of Bashar al-Assad, without the knowledge of the then defence minister.

The officers were believed to have gone to Syria in the hope of developing contacts and gaining information about Europeans in the country who had joined jihadi groups, although nothing was gained, according to media reports. The defence minister at the time, Steven Vandeput, has denied any knowledge of the operation. Some analysts believe the French intelligence may be involved, doubting Belgium would act alone.

After the Brussels attacks in 2016, Belgium’s warring intelligence services were urged by politicians to work together, but the latest reports suggest problems persist.

Bart Eeckhout, a senior writer at De Morgen, said the GISS was adept at espionage, “especially from each other”. In a comment article for the paper he described a service in the grip of permanent “office war”, characterised by mistrust, lack of direction and low morale among officers who believe resources are inadequate.

One source told the paper the service was in such disarray that it struggled to gather up-to-date information after the disputed elections in the Democratic Republic of the Congo, a key country of interest for Belgium as the former colonial power.

Neither Vandenborre nor the unnamed officer have commented on the allegations, although sources close to them have said the charges are baseless.

The allegations will fuel concerns about spying before the European parliament elections in May, which are already seen as a target for hostile powers.

The EU foreign service was even reported to have advised EU diplomats to avoid a popular Brussels steakhouse close to the European commission’s Berlaymont headquarters, prompting flabbergasted denials from the restaurant that any useful spying could be done in the noisy dining room.

The EU’s deputy Brexit negotiator, Sabine Weyand, made front-page news in the UK last summer when it was reported that she had raised the alarm about M16 spying on the Brexit negotiations. It emerged later that she had been joking.