In an update to his fellow borough councillors, Councillor Richard Cooper signalled it was not his intention to suspend funding to the organisation, adding that "throwing the baby out with the bathwater is not the way to go".
It comes after Sheffield and Hull councils announced they would withhold further funds for WTY until two independent inquiries into the organisation are completed, following the resignation of ex-chief executive Sir Gary Verity after an expenses scandal last month.
Addressing councillors at a full meeting of council, Coun Cooper praised the organisation for bringing "tens of millions" of pounds to the region via tourism.
"I'd like to make a very clear distinction between WTY as an organisation and what it does, and the governance issues it's currently facing," he said.
Police release CCTV image following report of voyeurism at Harrogate shop
New lights set to light up the Stray in Harrogate at iconic locations
Burglary at Nidderdale post office
Harrogate Convention Centre 'could lose £250 million without investment'
BBC team visit Harrogate as Harrogate Spring Water's expansion returns to spotlight
"Throwing the baby out with the bathwater is not the way to go.
"We should be supporting the hard working staff at WTY...therefore I regret that any councillor said that they'd be withholding membership fees or any other payments to WTY, I'd encourage them not to do that."
He said continuing financial support for the organisation was about supporting staff and making sure "we're a vibrant destination for tourism".
"I wholeheartedly support the staff there in all they've done...so it's not my intention to withhold any payments to Welcome To Yorkshire," he said.
He added that he supported "very much" the two independent investigations to be held into the organisation, with one set to focus on governance and human resources and the other centred on the agency's finances.
"I think there is further work to do to build confidence in the financial governance of the organisation, but what I don't think is that there's anything wrong with the organisation in terms of the work it has done around Yorkshire," he said.
He said the bulk of membership fees across 2017-2018 were paid by the Leeds City Region Business Rates Pool.
In 2017 the council paid £720 in event tickets and £844 in membership costs, followed by another £858 in membership fees in 2018.
Coun Cooper last week recommended that the group should publish details of all spending over £250 and open up board meetings to public scrutiny in a bid to restore public confidence in the private company.
Lachlan Leeming, Local Democracy Reporter