He was being sent for a scan today to assess the full extent of the damage, but the club are worried they could be without him for a vital chunk of the play-off push.
Jackson only won his first-team place back recently and started Saturday's 1-1 draw alongside Jason de Vos at the heart of the defence.
Ian Breckin, surprisingly dropped to bench, replaced him for the second-half.
Manager Paul Jewell said: "Jacko has a problem with his achilles and is sore.
"He picked up the injury out of nothing just before half-time and we'll now have to wait for the scan results.
"His head is down, he's on crutches, and it's a case of see what happens."
Latics found themselves out of the top six for only the second time in seven months after the Watford clash.
They trail West Ham, Millwall, and Sheffield United by just a point, though, and are three behind third-placed Sunderland – the in form side of the play-off chasers.
Jewell was disappointed with the result against the Hornets, seeing it as two points dropped rather than one gained.
But with the next two games coming against doomed Wimbledon and struggling Gillingham, there's every reason to believe Latics won't be out of the leading pack for long.
"It was a scrappy game, especially in the second-half, against a team fighting for their lives," said Jewell.
"I thought we started off well and were the better side early on.
"We went in front and had one or two other chances, and while we did okay, we didn't really do enough to win it.
"Don't get me wrong, we did all right and the effort was there, but we didn't do the basics well enough at times.
"We have dropped two points because the way we started the game, I thought we would be better than them."
Jason Roberts netted his fifth goal in Latics' colours to put the visitors ahead after 14 minutes.
But Heidar Helguson levelled 10 minutes later, getting above John Filan to head home.
Jewell said: "Jason scored a good goal from our point of view and he now has five for us. I felt we should have scored more because Jason de Vos was winning everything in the air in their box but we were never first to the second ball.
"For some reason we didn't show the desire to go in where it hurts at times. If we had got a second goal, we might have been okay, but we were never comfortable at 1-0.
"For their equaliser, John held his hand up after the game and said he made a mistake. He has saved us enough times, though, so everyone can live with one mistake."
Jewell admitted it had been a hard decision to leave Breckin out after he started all but two of Latics league games this season. "I told him on Wednesday that he wouldn't be starting and it was a tough one to call," he said.
"But with Jacko having this problem with his Achilles, Brecks came in and stood in well."
Source: Wigan Evening Post.