The Daggers played their fifth game in 14 days at the Globe Arena, with the last three of those successive away trips to Northampton, Accrington and then Morecambe.
Brian Woodall volleyed Dagenham into the lead after six minutes, but two second-half goals from Jordan Burrow and Andy Parrish snatched victory for the hosts.
Burnett said: "We have had a busy Christmas and were at Accrington at the weekend and I think the long journeys certainly had an effect. We looked jaded at the end and I think the miles caught up with us.
"We started well and looked comfortable after taking the lead. Our keeper (Chris Lewington) produced a couple of superb saves but they put pressure on us in the second half and despite the best efforts of the lads we couldn't hold on.
"There was no lack of effort but it was a heavy pitch and it certainly had an effect in the end."