Leeds United Supporters Trust and the Lions Trust have issued a joint statement following reports only 1,000 tickets would be made available for travelling fans in each leg.
Millwall lost at Carlisle to end up in fifth place while Leeds beat Northampton to finish fourth and the two clubs will now meet in the first leg at The 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.
Meanwhile, Cliff Byrne played a captain's role for Scunthorpe as they dramatically clinched a play-off place, while Crewe and Northampton were relegated after defeats.
Tranmere knew only a win against Scunthorpe at Glanford Park would see them leapfrog their rivals into sixth and they looked set to do so thanks to Craig Curran's 39th-minute goal. But Byrne popped up to head in the equaliser two minutes from time to send the Iron into the play-offs, where they will face MK Dons.
Leeds United condemned Northampton to relegation by beating them 3-0 at Elland Road, Luciano Becchio (44), the prolific Jermaine Beckford (59) and Robert Snodgrass (90) netting.
Crewe always looked unlikely to escape the drop with champions Leicester their final-day opponents, and the Foxes ended the season in style with a 3-0 win.
Bruno Berner (56), Lloyd Dyer (66) and Matty Fryatt (68) hammered the nails into Crewe's coffin, although as it turned out even a win would not have been enough to keep them up.
Carlisle were the big winners on the day as goals from Graham Kavanagh (7) and Paul Thirlwell (50) ensured United, who started the match in the bottom three, beat Millwall 2-0.
Brighton guaranteed their safety with a 1-0 win over Stockport, veteran Nicky Forster netting the only goal 17 minutes from time, while Hartlepool also escaped despite a 4-1 defeat by Bristol Rovers.
Peterborough, who secured their promotion last week, finished the season with a 2-2 draw at home to Swindon.
The prolific Simon Cox (17, 42) netted both Town goals but Craig Mackail-Smith (40) and Dean Keates (90) twice equalised for Posh.
Southend finished eighth after a 2-0 win over already-relegated Cheltenham, Adam Barrett (54) and Jean Francois Christophe (89) netting, while ninth-placed Huddersfield drew 1-1 with Leyton Orient.
Andy Booth gave the Terriers the lead in the 24th minute but Dean Morgan (65) levelled for Orient.
Oldham and Colchester both finished the season with away wins, over Walsall and Yeovil respectively.
The Latics had to come from behind for a 2-1 win after Troy Deeney gave Walsall a second-minute lead, Deane Smalley (44) and Ryan Brooke (74) sealing the points.
Colchester were comfortable 2-0 winners over Yeovil thanks to goals from Ashley Vincent (13) and Mark Yeates (15).