Despite making a number of smart saves, Harper was powerless to prevent the Magpies slipping to a 1-0 defeat at Villa Park on Sunday.
With Cheik Tiote and Kevin Nolan suspended, and Shola Ameobi nursing a knee injury that was assessed by the club's medical staff yesterday, Alan Pardew was short of options ahead of his side's trip to Villa Park.
The Newcastle boss was forced to field Fabricio Coloccini as a holding midfielder, and included the likes of James Tavernier, Michael Richardson and Ryan Donaldson on an inexperienced substitutes' bench.
With Andy Carroll's £35m fee burning a hole in his pocket, Pardew will attempt to add some depth to the ranks in the close season, and Harper admits the squad is currently being stretched to its limits.
"Injuries and suspensions are killing us really," said the shot-stopper. "You just had to look at our bench at Aston Villa to see how stretched the squad is.
"When you have as small a squad as we do, you can't really afford to be without three first-team players at the same time. We fancied our chances of getting something at Villa, but it undoubtedly became tougher when key men were out.
"To take three key players out of any team is a big ask, but to take them out of a squad the size of ours is a massive disadvantage.
"Cheik's back from suspension now, and hopefully Shola's injury is not too bad, but the size of the squad is undoubtedly an issue. It's all hands on deck at the moment."
Sunday's defeat leaves Newcastle seven points clear of the relegation zone with six games to go.
Villa were the only side in the bottom half of the table to win at the weekend, and with eight sides separating the Magpies from the relegation places, it is hard to see them being sucked into a battle against the drop.
Nevertheless, with matches against Manchester United, Liverpool and Chelsea still to come, Harper insists his team-mates cannot afford to take anything for granted in the final six weeks of the campaign.
"We still need more points and we know that," he said. "We have a few tough fixtures coming up now and we know we can't afford to take our eye off the ball.
"Man United is obviously a tough game, and then we have away games at Blackpool and Liverpool, which will be tough for different reasons. We'll need to dig deep there, but hopefully we'll have players back."
Manchester United are Newcastle's next opponents, with the St James' Park clash having been put back to Tuesday, April 19 because of the league leaders' involvement in the semi-finals of the FA Cup this weekend.
As well as taking on Manchester City at Wembley, Sir Alex Ferguson's side also face Chelsea in the second leg of the Champions League quarter-final tonight, and Harper is hoping their hectic schedule will play into Newcastle's hands.
"We have to hope the Champions League game and FA Cup semi-final take a bit out of them," he said. "They're flying in the league and it'll be a very tough game for us, but they have a big week coming up and hopefully they'll have two very tough matches."We'll have 52,000 roaring us on, and if we can get a couple of first-choice bodies back, we'll certainly have a chance."
Meanwhile, Jose Enrique's future has once again been thrust into the spotlight after former Liverpool defender Phil Thompson claimed a £15m summer switch to Anfield was a "done deal".
Liverpool's director of football strategy, Damien Comolli, has watched Enrique, who is about to enter the final year of his current Newcastle contract, on a number of occasions in recent weeks.
"From what I've heard, the deal has been done and he will come to Liverpool," Thompson told a Norwegian TV channel at the weekend.