When Victor Nilsson Lindelof made his first team debut for Vasteras as a 16-year-old in a 3-0 win over BK Forward in 2010, the Swedish third-tier club immediately knew they had a gem on their hands. The defender played a big part in their promotion that season but, inevitably, it did not take long for some of Europe’s superpowers to circle around the small city 90 minutes north-west of Stockholm.

In 2012 Benfica, the world’s 26th richest club, signed the teenager for a nominal fee – understood to be around €60,000 – with numerous add-on clauses factored in. Lindelof settled well, impressing in their reserve side, and eventually broke through to Benfica’s first team last year. “This is a dream,” he said on moving. Yet for his former club it has become something of a nightmare.

Now the criteria for one of those add-ons have been met Benfica have reneged on their financial agreement, namely declining to pay an additional €250,000 after Lindelof made 10 first-team starts in the Primeira Liga and Champions League. He made his 10th appearance in April.

Vasteras have made a formal complaint, which is pending, to Fifa’s players’ status committee. The Portuguese champions’ argument is that the agreement expired when Lindelof signed an updated contract in 2015 after breaking into the first team but Vasteras are adamant they are owed the money and are willing to go to court if the issue is not resolved by Fifa.

There is also a wider issue at play – if a ruling is made in Benfica’s favour it could see numerous other similar agreements between big clubs and minnows fall through.

As Lars Nilsson, the lawyer acting on behalf of Vasteras, told the Guardian: “This is not just a legal issue, it is also a moral and ethical issue. It is sad for a small club that are dependent on this money for their future but that’s the way it is when small clubs come up against big European clubs.”

Nilsson expects Fifa to rule in Vasteras’s favour even if he is dismayed by the Players’ Status Committee taking its time over the complaint. He had sent documentation to the governing body four weeks ago but as of the end of last week it had not been forwarded to Benfica.

Vasteras, who play Swedbank Park, are unable to move up the Swedish pyramid because of their debt. Photograph: Getty Images/Bongarts/Getty Images

“I’m rather disappointed,” Nilsson said. “Fifa have still not sent our submission to Benfica for a response. They promised to do it within a short time – but what that means exactly is up to each person to decide. Normally they ask to respond within 20 days but that would be prolonged if Benfica have a legitimate reason to hold it up.”

However Benfica, who have not been in contact with Vasteras since rejecting an invoice for the €250,000, have reaffirmed their reluctance to pay the fee. “Vasteras expressly and irrevocably assigned to Benfica the entirety of the player’s registration and economic rights as of 18 July 2012,” a spokesperson said, adding that “clause six of the agreement signed between the two clubs mentions that ‘as a consequence of this definitive assignment of rights’ the player Victor Nilsson and his legal representative undertake to enter into a sport labour contract with SL Benfica to be in force from 18 July 2012 up to 30 June 2015.”

Benfica are basically saying that because Lindelof has signed a new contract the initial agreement between the two clubs is void.

Vasteras’ vice-president, Christina Liffner, said they have received support from the Swedish Football Association, who had signed off on the transfer when it was made five years ago, but is keen for the matter to be resolved quickly. “I’m afraid it could take one or two years for a decision to be made,” she said. “That’s very bad for us because we are a small club and we need this money.

“In reality they should have paid up without us asking for it. But when we sent them the invoice they simply said they declined to pay us. They say the contract is no longer valid but after speaking to many lawyers and experts we are convinced it is.”

The money would clear Vasteras’ debts, which currently make it impossible for them to be promoted. Rules in Sweden stipulate any club unable to show a profit in their most recent accounts cannot be elevated in the pyramid. They finished sixth in the Division One Norra this season having been relegated after one season in the Superettan.

Victor Nilsson Lindelof celebrates with after winning the Portuguese League Cup in May 2016. Photograph: Gualter Fatia/Getty Images

Benfica’s most recent published accounts show a turnover of €126m, making them the world’s 26th richest club according to Deloitte. The 35-times Portuguese champions have almost half a billion in assets and several members of their current squad earn more in a month than Vasteras’s annual turnover of €660,000.

“We are a small club,” Liffner added. “Clearing our debts is essential because to go up the ladder in Sweden we need to have positive equity. The money would not be to buy players; it would be to balance our accounts.”

Further complications could also arise if Benfica decide to offload Lindelof in the future because the initial contract included another clause entitling Vasteras to a percentage of any sell-on fee. In January of this year he was close to joining Middlesbrough but the move was held up despite all parties agreeing a transfer in principle. It is not clear whether there is a link to the Vasteras dispute.

He is contracted to the Lisbon club until the end of the 2019-20 season and his market value has risen considerably since consolidating his place in Rui Vitória’s defence. The 22-year-old has also become a mainstay of Janne Andersson’s Sweden team in 2016.

Lindelof’s representatives did not respond when asked for a comment.