Amond levelled when he nipped in front of his marker to flick a Ryan Williams free-kick past the excellent Chris Lewington.
Shrimps skipper Hughes then put the home side ahead when he lashed home the loose ball after the Dagenham defence had failed to deal with another dangerous Williams corner.
Dagenham pushed bodies forward in search of an equaliser and Rhys Murphy was denied by a stunning save by Barry Roche on 88 minutes but the former Arsenal youngster maintained his recent run of good form with a fine near-post finish from Zavon Hines' late low cross.
He commented: "When you are 2-1 up in injury time you expect to win games and we are all obviously disappointed not to have another two points and it feels like a defeat.
"The lads were all distraught in the dressing room after the game because they wanted to have a fifth successive win and thought they had done enough to get it.
"After another slow start where we conceded first again, we controlled the game for long periods and had it not been for their keeper we could have scored a few more and had the game won.
"But you have to give Dagenham credit as well because I thought their late equaliser was a really well-worked goal and sometimes you have to hold your hand up and admit that."
- Sports & Recreation
- Padraig Amond