The Hammers tumbled back into the bottom three on Saturday after going down 3-1 at home to Newcastle United.
It had been suggested in the build-up to the game that Carroll may be offered a starting berth against his former employers.
He made his long-awaited return to action after foot and ankle problems in a 2-0 win at Cardiff City, but is being forced to make do with a place on the bench as West Ham favour a cautious approach when it comes to his long-term fitness.
On his decision to give Carroll half-an-hour against Newcastle, Allardyce told Sky Sports: "I don't care what anyone says, we do what we have been doing all season - it's the medical side that decide on how we get Andy Carroll back fit and playing, not anyone else.
"My decision, via the medical process, says that if you risk any more than that, then you risk the lad getting injured again. Is that what we want?
"He is our biggest major asset that we have signed and we want him on the pitch playing every week. We have to do that slowly.
"Irrespective of how desperate it gets, it's more about making sure Andy stays fit for the entirety of this season to try and help us get some results than it is to risk him for another 15 minutes and get him injured again."
Carroll spurned one glorious opportunity to level matters when West Ham trailed 2-1, but Allardyce believes it is issues at the back - where he continues to be denied the services of key senior performers - which are costing his side dear.
He said on a 12th defeat of the season: "We had quite a bright start and had we shown a bit more quality in the final third, we might have caused more problems. We didn't get a chance in that period and then the two goals were a lot down to our deficiencies rather than the opponent's play.
"We came fighting back from that and got a lifeline just before half-time with the goal, and the second half we piled the pressure on but couldn't convert the chances that we created.
"Again, it's really disappointing because I keep telling the players and reminding them that this period is difficult because we haven't drawn enough, never mind won enough. You always set out in games thinking if you can win it, that's great, but make sure you don't lose it. We are losing too many and we have got to put that right as quickly as possible.
"What will help us put that right will be suspended players back - James Tomkins and Kevin Nolan - and injured players as quickly as we possibly can.
"George McCartney ended up with a severe neck problem this morning, worse than we expected, so he couldn't be selected. We put Matt Taylor in at right-back and two central defenders who had never played together before, so it's a difficult period for us in the defensive side of it and I think that's the reason why we conceded three goals today - not that they didn't try really hard, just the unfamiliarity in our defensive unit at the moment.
"Because it has to change every week, that is causing us a few problems in terms of the goals that we're conceding. At the other end, we haven't scored enough all season."