The controversy overshadowed a fine win for England which was inpsired by a Jodie Taylor hat-tick against an Australian side that was full of confidence after a 1-0 win over Netherlands to commence its group campaign.
An Army contingent based in Cyprus attended the game in Nicosia on Friday (local time) and two female England supporters who were at the game said the troops targeted Matildas defender Servet Uzunlar throughout the match, as well as the Australian team's substitutes as they took off their tracksuits before entering the field.
Rachel O'Sullivan and Sophie Downey, who cover women's football for , said the majority of the alleged abuse was made towards the Australian players and substitutes, whose bench was on the side of the pitch where the soldiers were sitting.
"We've been to lots of games before and we can engage in banter, but this wasn't banter - it was constant, gender-specific abuse," Downey said.
"There were around 50 troops watching the game and a group of around 10 of them were directing constant insults - they were on the side of the Australian dugout so it was more focused on their players.
"We weren't sure whether to tweet about it because it's the Army and we didn't want to offend people - I'm a very proud English person and I'm very proud of what the Army do - but I was ashamed of them today."
O'Sullivan added: "One Australian player, number six (Uzunlar), they were harassing her over and over and over again, throughout the game.
"They were making horrible comments, shouting at her, whistling - it was uncomfortable to hear. These are teenage girls and they were sexually objectifying them."
This occurred the same day FIFA president Sepp Blatter called for greater equality between men and women within the higher reaches of world football's governing body.
A spokeswoman for the Ministry of Defence said: "Behaviour of the kind described is totally unacceptable and is not tolerated in the Armed Forces where abuse, bullying and discrimination have no place.
"We are investigating these claims and if it is found that any UK personnel have fallen below the high standards we expect then appropriate action will be taken."
Downey and O'Sullivan said they complained to the commander in charge of the contingent at the end of the match and he apologised, saying he had not heard the abuse.
An FA spokesperson told Press Association Sport: "We've spoken to the (England) players, manager and assistant manager after the game and none of them have said they heard anything during the game worthy of reporting or complaining about.
"They appreciated the British Army's support and were happy to have photographs taken with the Army boys at the end of the game."
An Australian supporter at the match, who wished to remain anonymous, said: "This was a stunning one-off that I've never heard before in women's football.
"They were calling the girls t****, telling the referee 'I'd like to b*** you'.
"I said something to the Army sergeant, 'This isn't a complaint as an Australian supporter, it's a complaint as a woman'. It was beyond the pale.
"He was apologetic after the game and offered to apologise to the players.
"He said they're just a bunch of young boys, but I have 17 and 18-year-old brothers, I know what they're like but they wouldn't say that to strangers."
The controversy comes after recordings of were broadcast by the BBC on Thursday night, prompting the London club to call for an end to sexism in football.