Hughes lobbed home Gareth Williams' pass just after the half-hour to give Leicester a deserved half-time lead.
Millwall pressed through a succession of David Livermore corners, one of which forced Paul Henderson to tip away Paul Robinson's close-range header.
But Millwall couldn't add to their 11 goals at home and remain third-bottom.
"If I was a betting man I'd bet on us to stay up.
"We performed well and put them under a lot of pressure in the second half but couldn't put the ball in the net.
"I will be trying to get a striker in before the loan deadline passes this week."
"We're not safe yet and we must keep our focus.
"This league is unusual with the results recently - look at Sheffield Wednesday beating Preston.
"The players have been magnificent for me and they were again."
Millwall: Marshall, Lawrence, Vincent (Hayles 58), Whitbread,
Paul Robinson, Elliott, Dunne, Livermore, Cameron, May,
Asaba (Williams 31).
Subs Not Used: Doyle, Phillips, Braniff.
Booked: Whitbread, May.
Leicester: Henderson, Kisnorbo, McCarthy, Johansson, Stearman,
Maybury, Hughes, Williams, Gudjonsson, Hume (Welsh 84),
Fryatt (O'Grady 66).
Subs Not Used: Douglas, Brevett, Gerrbrand.
Booked: O'Grady.
Goals: Hughes 31.
Att: 10,523.
Ref: M Thorpe (Suffolk).