Seven members have not yet turned up, allegedly because of transport issues.
But there are suspicions the Algeria team wanted to boycott the match against Israel because of longstanding tensions between the two countries.
Goalball is a sport for the visually impaired involving a ball with bells.
Algeria had been due to play the US on Friday, and Israel on Saturday, and the seven team members were scheduled to leave a training camp in Poland for Rio last Monday.
The IPC says the team claims to have missed a bus which led to them missing a flight. They allegedly did not manage to rebook it in time because of a public holiday in Algeria.
"It's an interesting account they have delivered to us," IPC spokesman Craig Spence told the BBC.
"To have five days travelling to Rio, it's a long time. I've missed connections in the past, and you usually get there within 24 hours," he said.
Goalball at the Rio 2016 Paralympics: All you need to know
A beginner's guide to goalball
The Times of Israel suggests the Algerian absence is "likely to avoid an Israel draw".
"It is a great shame that politics has also seeped into the Paralympics," the paper quotes the head of the Israeli Paralympic Committee, Danny Ben-Abu, as saying.
The issue has received some reaction on social media too.
The IPC says it will check the facts and act accordingly.
"If, as many people believe, this is a political protest, we can take some form of action against them," Craig Spence says.
"It could be a slap on the wrist, or we could remove the goalball team from the tournament altogether," he added.
In the meantime, both the US and Israel have been awarded a 10-0 win and three points each for the unplayed matches.
Goalball is played by two teams of three visually impaired players, using a ball with bells inside.  The object of the game is to throw the ball into the opposing team's net, while defenders attempt to block it with their bodies.

Suffolk Fire and Rescue Service, which employs about 700 people, may also lose 50-60 on-call firefighters as part of the savings plan.
The number of full-time crewed stations was reduced to four in a previous round of cuts - two remain in Ipswich, along with Lowestoft and Bury St Edmunds.
A public consultation on Suffolk County Council's plans will now take place.
Seven of the county's 47 fire engines could be scrapped and Wrentham fire station may close as part of the £1.3m cuts.
A fire engine in Sudbury, where a major fire broke out in September, could be replaced with a smaller "rapid response" vehicle.
Matthew Hicks, of Suffolk County Council, said he was confident an "outstanding service" could be maintained.
"Without question, this is a challenging set of proposals," he said. "However, they have been shaped by the feedback we received during the recent pre-consultation held in the summer.
"I now encourage people to respond to this full consultation so we have a wide range of views to inform our final decisions."
There has been a fall in the number of emergency calls over the last 10 years in Suffolk, in line with other authorities, from about 10,000 in 2004 to about 6,700 last year.
A spokesman for the Suffolk Fire Brigades Union said they were "deeply concerned about the devastating cuts" which, they said, were "nothing but dangerous".
Chairman Andy Vingoe said: "The £1.3m saving could be avoided totally if council tax was increased by less than £1.80 per person in Suffolk per year.
"We strongly urge all residents to reply to the consultation to tell the council that we are not prepared to endure these cuts."

Jacqueline Carol Lloyd, 46, died after being struck by an out-of-service bus on Butts Lane, Southport, at about 23:50 BST on 17 May 2015.
Derek Bebbington, 57, of Moss Nook, Burscough, denied the charge during a hearing at South Sefton Magistrates' Court.
He will appear at Liverpool Crown Court on 10 June.
The International Paralympic Committee (IPC) has said it is investigating why the Algerian women's goalball team failed to arrive in Rio in time for matches against the US and Israel.
[NEXT_CONCEPT]
Twenty full-time firefighters could lose their jobs in Suffolk in order to meet budget cuts of more than £1m.
[NEXT_CONCEPT]
A man has pleaded not guilty to causing death by careless driving after a woman was hit by a bus in Southport.