The eels came up on the Masterton District Council's agenda in February, with councillors voting to support the relocation of the population by creating "ladders" - coarse matting - for the eels to crawl along, and a connecting pipe.
Trapping and relocating the eels was considered a fall-back option, but it turns out this has been employed to shift around 2000 eels.
Assets and operations manager David Hopman said they were in conversation with local iwi and were going to pursue the eels that were left.
"There's been a small number of deaths," he said. "Our objective is to minimise this."
"We've relocated about 2000 using nets, which fill up each night."
He said there was never 85,000 full-grown eels, but if you counted small eels, there was a big number overall.
'Spate ropes' had been used to help young eels (elver) relocate, and coarse matting would be employed in migration season.
Mr Hopman said there had been no need to have a transfer pipe.
"Eels are very good at climbing out of ponds.
"But we're still catching them, and relocating them, and we will continue to do so."
Deputy mayor Jane Terpstra said council officers had been working with the environmental manager for Ngati Kahungunu ki Wairarapa, Ra Smith.
Mr Smith had previously discussed the importance of the eels to Wairarapa Maori and wanted to ensure they would be looked after.
The Times-Age was not successful in contacting Mr Smith for comment.