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.
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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.
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.