Cowan, who debuted as captain for the side last year, was targeted by the Blues to move north in a deal which would had seen him loaned back to the Southland side.
But the All Black halfback is believed to have decided to stay in the South for another season.
Cowan's agent did not return calls yesterday and Cowan could not be contacted.
Cowan (27) may have been put off moving north with the Blues in-fighting over player payments and the scheduling of matches for next year's Super 14 and beyond.
Highlanders chief executive Richard Reid said he had not heard from Cowan about any move north and these sort of rumours were normal at this time of year.
It would be disappointing if Cowan left but it was just all speculation at the moment.
Reid met Southland Rugby Football Union chief executive Roger Clark, Highlanders coach Glenn Moore and new Highlanders board member Mike Eagle in Invercargill late last week.
Reid said the future of Cowan was discussed, as were a lot of other things.
Players had until October 16 to decide on transfers to another franchiseSouthland prop and captain Jamie Mackintosh, who was vice-captain of the Highlanders last season, is weighing up an offer from the Hurricanes.
He confirmed that over the weekend, saying he had the option of going elsewhere and then staying in Invercargill to play for Southland.
Mackintosh (24) said pushing himself in a new environment could well be exciting for him.
He was due to make a decision this week, but is believed to be under some pressure to remain loyal to the Highlanders.
His contract with Southland is up at the end of this season.
Eagle said it would be disappointing for the franchise if both players disappeared.
"They need to stay there as they are vitally important for the franchise.
It won't look good if they are walking away from the place," Eagle said.
"Serious questions have to be asked about the environment if two home-grown players, both of "them good Southland boys, walk away."
With the Highlanders being backed by the New Zealand Rugby Union for the next couple of years, it would appear illogical for the national union to let the players leave.
Moore declined comment.
Clark had earlier said Cowan had a contract with Southland and the New Zealand Rugby Union which was not due to end until the end of next year, and he had not heard from Cowan.
Cowan is available for the Southland side this week after finishing his leave period from the All Blacks, and is likely to play for the side in what is shaping as a must-win match against Tasman in Invercargill on Saturday.
