BBC Two's Newsnight programme reported that a police probe in Belgium had concluded that the Premier League club, losing Champions League finalists this year, had paid Beveren 1 million pounds ($1.87 million).
It said world body FIFA were investigating whether Arsenal had breached rules concerning fair play and conflict of interest.
The North London club, in a statement to Newsnight, confirmed a technical relationship with Beveren since 2001 but denied controlling the club.
"Arsenal confirms that it has never owned, directly or indirectly, any shares in Beveren or had any power whatsoever to influence its management or administration," it said.
"It did in 2001 provide funds of 1,570,703 euros by way of a loan to a member of the consortium to assist in stabilising the finances of Beveren.
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"Arsenal and all its staff have acted properly throughout, in accordance with all applicable rules and regulations, and in the best interests of Beveren, Arsenal and the broader footballing community."
Newsnight said the Belgian investigation was launched initially because the police suspected the Russian Mafia might be using Beveren to launder money. That was later ruled out.
The BBC programme said Beveren was used to bring Ivory Coast players, including Arsenal's Emmanuel Eboue, into Europe.
