The 2003 World Cup star, who joined English County side Warwickshire last year after his heroic performance in South Africa, fell ill after bowling in his team's three-day game against Pakistan 'A' at the Nairobi Simba Union club.
Kenyan team coach Andy Moles said Obuya would undergo surgery on Monday and may be doubtful for the Champions Trophy in England in September.
"He is likely to be out of action for seven weeks. It is a great shame because Collins has played good One-day cricket for Kenya," said Moles.
He said Obuya's illness may have contributed to his below-par bowling against Pakistan 'A' when he failed to take any wicket in the tourists' first innings.
Obuya's absence on Monday meant Kenya were one player down when they resumed batting on the third and final day when they were behind by 231 runs.
The home team were already without the services of off-spinner Maurice Odumbe who opted to take a break following an inquiry into match-fixing allegations.