Wigan's opening match of the season against Chelsea will definitely go ahead after the club settled an outstanding police bill of £273,062.
But Wigan say they paid "under protest" and hope to recover the money.
A club statement said: "In making this payment Wigan will make no admission of liability whatsoever."
Greater Manchester Police threatened not to police Wigan games if the bill was not paid by 1 August, but Wigan say the charges are unfair.
Wigan chairman Dave Whelan claims the bill was not in line with other teams in the area and he is determined to pursue a counter-claim.
The statement continued: "We accept that policing charges have to be paid but maintain they should be fair and reasonable.
"The club's position in this position has not changed but in order to ensure that football is not disrupted by any action we have decided to pay the sums claimed in full but under protest.
"I feel I am fighting for all the teams in the lower divisions to get reasonable charges"
"Our lawyers have been instructed to vigorously pursue a counter claim against the police to recover the sums paid under protest, together with damages.
"The claim is likely to be based on the combination of breach of contract, infringement of competition law and the unlawful exercise of the police powers."
Whelan claims Wigan were charged £44,000 to police last season's home match versus Leeds United while Preston North End - which comes under Lancashire Police's jurisdiction - was charged just £7,000 when they played the same opponents.
He said a Home Office investigation was under way into police charges for football matches across the UK.
Whelan warned the Football League would be in grave danger of collapsing if he were to lose a test case in the High Court.
He said: "If we were to lose and the police were given the authority to charge what they wanted throughout the nation you could say the Football League is finished. It is as serious as that.
"I know a lot of clubs in the Football League are scared of their bills.
"I feel I am fighting for all the teams in the lower divisions to get reasonable charges."
Wigan's Premiership debut against Chelsea is due to take place on 13 August.
If the police had carried out their threat not to police Wigan's home games, the club would not have been able to play at the JJB Stadium.