The U’s boss was frustrated by his side’s performance as they suffered a disappointing afternoon at Sixfields, conceding early in both halves to goals from Matty Warhurst and Sam Hoskins.

Colchester were playing their third game in a week and their second successive away fixture, having also had to contend with a growing injury list.

But Cowley insisted those factors could not excuse the U’s display and challenged his players to be physically ready for the demands of a long season.

“It was a tough day and we’re going to have tough days, this season - that’s the truth,” said Cowley.

“It was the third game in a week and two away games, back to back, four out of five away from home.

“They’re all excuses that no-one wants to hear but when you go down and in particular concede a second in these three-game weeks, you can feel sorry for yourselves and being honest for the players, it’s always tough.

“We’ve got a lot of injuries at the moment and we’ve had to go again and again.

“It’s easy when it gets tough and the second goal goes in just to feel sorry for yourself in that moment.

Thanks - Colchester United assistant head coach Nicky Cowley applauds the U's fans at Northampton (Image: Richard Blaxall)

“But we tell them all the time - they’re professional footballers and their responsibility is to be fit and available for 46 league games and however many cup games that you play.

“Often, in that nine-month period there’ll be a lot of times when you have to play three games in a week and you have to be physically ready to do that.

“I didn’t think we were which is frustrating and a concern.”

Cowley was also forced to gamble on the fitness of some of his more experienced players.

Bez Lubala had trained only once ahead of the game and was still experiencing swelling in his knee, while Jack Payne attempted to make himself available after coming through training.

Lubala started and Payne came off the bench - but Cowley conceded Payne was “not right” and accepted responsibility for his team selection.

“It’s tough at the moment; Bez has just trained once yesterday, he did his best but he’s still got some swelling on the knee,” he said.

“Jack Payne wants to help, trying to do the right thing by making himself available, came through training and we’re all hoping he’ll be OK but he wasn’t right.

“They’re good boys and they’re doing it for all of the right reasons - the responsibility has to come to me, because I pick the team but I’m trying to help the seniors who need some help by putting a couple more out there.

“It didn’t work and we have to take responsibility for that.”

Stretch - Ellis Iandolo in action for Colchester United against Northampton Town (Image: Richard Blaxall)

Cowley was particularly unhappy with the manner in which Colchester began both halves.

The U’s started slowly, conceding in the ninth minute to what their head coach described as a “really soft goal”.

Colchester improved during the remainder of the first period and created opportunities for Ben Perry and Bradley Ihionvien.

But any hopes of building on that response were badly damaged when Northampton struck again shortly after the restart.

“It was a really tough day for us,” said Cowley.

“A really poor start - we didn’t get out of the blocks, didn’t make any tackles, didn’t compete, couldn’t put two actions together in the first 10 minutes, we then conceded a really soft goal.

“So, a poor start and then a good response but it’s a really bad strategy when you have to get punched on the nose, before you respond.

“We responded and put a good period together.

“We create a good chance for Ben Perry from Oscar’s cross and then Bradley has a chance and he just has to score, which was such a good opportunity.

“It was a really tight first half with not much in it.

“I certainly don’t think there was much between the teams, when you look at the chances.

Setback - Colchester United's Jack Payne at the final whistle at Northampton (Image: Richard Blaxall)

“We got in at half-time, tweaked a few bits but came out in the second half and conceded straight away again.

“I’ve been a manager for 20 years and when you go 2-0 down away from home, I can probably count on one hand the number of times a team comes back and gets a positive result, so it was a really poor start to both halves.”

Cowley also apologised to Colchester's 600 travelling supporters, admitting they had been given little to cheer.

He added: “They were really good - I feel really bad for them.

“They got up early, did their very best, got behind the boys and we gave them very, very little.

“We’ll get heavily criticised and rightly so and we have to suck it up, accept it because we didn’t do enough for them today.”

The defeat extended Colchester's winless League Two run to nine games, while Northampton had started the match second-bottom in the division.