The All Whites face Oceania champions Tahiti in Papeete on Friday in their third match of the final round of Oceania World Cup qualifying for the 2014 finals in Brazil.
Queens Park Rangers' Nelsen suffered a knee injury and West Ham United's Reid had back spasms in the Premier League last weekend but New Zealand Football had been hopeful the pair would arrive in time for the match in Papeete.
On Wednesday, however, Herbert said he was planning to be without the duo and instead hoped they would be available for the fourth match in Christchurch on October 16.
"We'll work around Winston and Ryan being with us in Christchurch because I think the timing will mean they won't make it to Tahiti," he said. "It will be a chance for some other players to step up which will be good and I think we'll be fine.
"I'm comfortable with the depth of the squad and we have a couple of different pairings that can play at the back.
"Leo Bertos is an option at right-back which gives us the ability to play a back four but we'll see."
The All Whites leave Auckland on Thursday for Friday's match at Stade Pater before both sides travel to New Zealand for the game in Christchurch.
Nelsen, who was born in Christchurch, had been especially keen to play the match at Rugby League Park in Addington as it would have been his 50th 'A' international if he also played in Papeete.
Nelsen and Reid have formed an effective combination with Ipswich Town's Tommy Smith in Herbert's 3-4-3 formation and their absence in Papeete will likely see Wellington Phoenix duo Tony Lochhead and Ben Sigmund come back into the line-up.
The All Whites, who crashed out of the Oceania Nations Cup in June and missed a lucrative payday at the 2013 Confederations Cup, lead the group after wins over New Caledonia and the Solomon Islands, who clash in Honiara on Friday.
Tahiti have lost both their games and are last in the group.
The fifth round of matches will be held next year, with Tahiti hosting the Solomon Islands, while New Zealand host New Caledonia on March 22, with the final matches on March 26.
The winner of the pool will face the fourth-placed team from the North and Central America and Caribbean region (CONCACAF) in a two-legged playoff for a spot in Brazil.
