Williamson retired hurt with a hamstring injury during the second T20I in Hamilton on Sunday.
Williamson, who scored 26 off 15 balls, felt tightness in his right hamstring, the same leg as his previous knee injury. He has returned to Tauranga for a scan, and while he was already set to miss the third match, his participation in the last two games remains uncertain.
The 33-year-old endured a tough time with multiple injuries in recent months. He suffered an ACL rupture in the opening match of the IPL 2023 season while playing for Gujarat Titans, leading to his absence from competitive cricket for more than six months.
The Kiwis are prioritising the upcoming two-match Test series against South Africa, slated to get underway on February 4.
New Zealand head coach Gary Stead expressed concerns about Williamson's injury, saying that a further decision would be made after the scan results.
"It's the same leg as what his knee injury was on. He's gone home to Tauranga. He'll get a scan today,” ESPNCricinfo quoted Stead as saying.
"Until I know more about the scan, then I haven't got any further update at this stage. Will Young was going to join the team anyway for this [part of the] series. Kane wasn't going to join. I think it's likely that Will will stay on, but until we get the scan results from Kane, then we can't make a further decision."
Asked if Williamson would participate in the final two T20Is, Stead said: "I think it's unlikely he will play. I mean with the Test matches so close as well and probably in the big scheme of things in the short term for us has higher priority then I think it's likely we'll try and make sure that he's right for that."
In Williamson’s absence, Tim Seifert is likely to step in and take the keeping duties from Devon Conway.
"It'll be another test without having Kane there, who I think always provides that stableness to your batting. That'll be an opportunity for, likely, Tim Seifert to come in and show what he can still do, and fill in those shoes that Kane's probably left for the rest of the series," Stead said.
The third T20I between New Zealand and Pakistan is slated to be held in Dunedin on Wednesday (January 17).
(ESPNCricinfo Inputs)