Millwall lost at Carlisle to end up in 5th place while Leeds beat Northampton to finish 4th and the two clubs will now meet in the first leg at The New Den on Saturday, May 9 and at Elland Road in the return on Thursday, May 14.
The statement read: "Supporters who have regularly travelled the length and breadth of the country to follow their teams deserve every opportunity to attend these matches.
"For this reason, the Lions Trust, in tandem with the Leeds United Supporters Trust, are calling on the management of the clubs and police commanders involved to work with fans to make both matches the fantastic occasions they deserve to be.
"The difficulties of policing important football matches and the security problems that they impose is of course recognised and acknowledged.
"We have every confidence, however, that the Metropolitan and the West Yorkshire police forces have both the professionalism and experience to be able to handle what remain, after all, third-tier level football matches."
Both fans' groups argue restrictions could force visiting fans to obtain tickets in the home sections, potentially causing more problems.