The 20-year-old Cardiff City loanee was making his first start since joining Northampton earlier this month but had to be replaced by Danny Rose after an hour.
Whilst the problem was not thought to be serious at the time, further investigation has revealed otherwise.
Manager Jon Brady said: "I didn't want to take Chanka off on Saturday but he felt his hamstring and we had to look after him and now he's out for six weeks with an injury.
"That's really, really frustrating for us. We managed him so well, we integrated him into the side and we had to look after his training loads because he's come from U23s football.
"But then he makes his first start for us and has to come off after 55 minutes because of his hamstring.
"He kept telling us that it was just tight and that's the level of commitment Chanka showed us because he wanted to keep pushing and keep playing.
"But we sent him for a scan and he's out for six weeks."
Meanwhile, captain Joseph Mills might have to wait a little longer to make his first appearance since September.
Brady added: "Millsy has had a setback with his ankle. We had to train on the astro turf because it was frozen and he's unfortunately missed training all this week."