Vincent Tan's level of interference in his role as Cardiff City's owner has extended to signing a player without the prior approval of Malky Mackay or any of the manager's recruitment and scouting staff. Etien Velikonja, a Slovenian forward who cost €2m (£1.7m), arrived at Cardiff unannounced last year and via a deal that involved Jorge Mendes, one of the world's most high-profile football agents.

Velikonja signed a four-year contract when he joined from NK Maribor in July 2012 but has played only 73 minutes of league football in 15 months and completed only one game, when he was named in the starting XI for the 2-1 FA Cup defeat at Macclesfield in January. The 24-year-old, who earns a five-figure weekly salary, has not made the substitutes' bench once this season and, based on his transfer fee alone, has so far cost Cardiff £10,000 for every minute that he has played.

There is no suggestion that Velikonja or anyone else is guilty of any wrongdoing, with the player oblivious to the strange circumstances in which he signed for Cardiff, who were a Championship club at the time. Velikonja's transfer does, however, raise fresh questions about Tan's approach and the way he is running the club. It also brings up comparisons with Bébé – who famously joined Manchester United for £7.4m in 2010 and never started a league game. Bébé was represented by Mendes.

Only a fortnight ago the Guardian reported that Tan – who recently claimed that his investment in the club stands at £125m – has tried to pass messages from the stand during matches, including suggested tactical changes and substitutions. In another embarrassing development it was revealed that Alisher Apsalyamov, a 23-year-old from Kazakhstan who was controversially appointed as Cardiff's head of recruitment after Iain Moody was sacked in October, has been forced to stand down from his position while the Home Office investigates his work permit.

The Velikonja deal opens another can of worms. It is understood that the transfer came about after Velikonja's name appeared on a list that Tan returned to Cardiff with after he had met Mendes in the summer of 2012. Although Mackay had been interested in signing Velikonja several years earlier, when he was in charge of Watford, Cardiff had bigger ambitions and were operating at a different level to his former club in the transfer market because of Tan's determination to win promotion to the Premier League. The Guardian understands neither Mackay nor Moody wanted to sign Velikonja for Cardiff.

Yet within a couple of days of Tan producing the list, a deal for Velikonja had been completed and the player arrived at the club's training ground accompanied by Joao Camacho, an agent who works for GestiFute, Mendes's company.

Zlatko Zahovic, NK Maribor's sporting director, refused to disclose at the time how much Cardiff had paid for Velikonja but said that it was a record sum for a Slovenian footballer. The fee registered on the Transfer Matching System, which was introduced by Fifa to bring greater transparency and enable clubs to confirm the terms and conditions of player transfers, is €2m. Some at Cardiff feel that the figure was way above Velikonja's market value.

In an interview with a Slovenia newspaper last December, Zahovic, who had a distinguished playing career that included spells with Porto, Olympiacos, Valencia and Benfica, confirmed that he negotiated the fee for Velikonja with Mendes. "Not even a big agent like Jorge Mendes can outsmart me," Zahovic told DNvevnik. "His first bid for Velikonja was €600,000. At the end they paid €2m. Mendes did not know that I knew what the club could offer. I knew exactly how much they could pay. In my job one has to be informed."

Zahovic told the Guardian this week that he did not know if Mendes was working on behalf of Cardiff. "I don't know, you must ask him. He was making negotiation between Cardiff and Maribor, nothing else."

Asked whether he had ever had any contact with anyone at Cardiff about Velikonja's transfer, Zahovic replied: "No, nobody." When questioned about the size of the transfer fee, Zahovic denied that it was high and said: "This price was special for Cardiff, because I think his value is more than €2m." Zahovic claimed to know nothing about whether Tan signed the player without Mackay knowing. "I don't know. This is not important for NK Maribor. This is a problem of Cardiff."

It is unclear what precise role Mendes and Camacho had in the transfer, whether they acted as official agents in the deal and whether they were paid by any of the parties. As for Velikonja, he has not played for Cardiff since the final day of last season, when he was given his first league start in a game that meant nothing to the Welsh club because they had already been crowned champions. He was substituted at half-time.

The Slovenia international publicly stated his desire to leave in August – "I want to move somewhere where I will play, as I surely won't get any chances at Cardiff" – but the Premier League club have struggled to find anyone to cover his wages. One offer from overseas would have left Cardiff paying virtually all of his salary.

Back in Slovenia, Velikonja's situation is viewed with a degree of bemusement. "As a young boy here in the Slovenian league he was the best scorer when he was 18," said Robert Vrtovec, president at ND Gorica, Velikonja's first club. "He had an injury and after recovering it was not the same Velikonja as before. But at Maribor he made big progress and he scored some important goals in the Europa League.

"The value of Velikonja before he was injured, we had offers of more than €1m for him. He was 18 then. It's difficult for me to judge. If I am a person who is not a buyer, I would like to have as much money as possible. If the buyer is stupid that he buys a player who, for example, is valued at €500,000 for €2m, it is his problem."

Both Cardiff and GestiFute failed to respond to questions about the transfer despite repeated requests from the Guardian.