It said the deal’s significance “cannot be underestimated”, but the value and structure was commercially sensitive.
Releasing it would be likely to create an “expectation” other companies would be entitled to a similar deal, it said.
Tory Assembly leader Andrew RT Davies said ministers seemed to be “hiding behind commercial confidentiality”.
Direct flights began between the Welsh government-owned Cardiff Airport and Doha in Qatar in May.
First Minister Carwyn Jones called it a “huge boost” for Wales which would open up links to the rest of the world.
The two-year marketing partnership between the Welsh government and Qatar Airways, which was revealed in March, will see “extensive activity in key markets to raise the awareness of routes into Cardiff Airport”.
The Welsh government and Qatar Airways will monitor and audit the deal’s value for money.
Under the Freedom of Information Act, BBC Wales asked the Welsh government to provide the cost and structure of the partnership to market Wales internationally as a business and tourist destination.
It refused to release the information on the “unique” deal on the basis it could prejudice the economy of Wales, and compromise the commercial interests of Qatar Airways.
“The release of this information… would place into the public domain highly sensitive and current commercial information which is still being relied upon by the Welsh government in negotiating similar deals with other companies,” it said.
“The economy of Wales is interlinked with the success of this deal and its significance and subsequent success cannot be underestimated in this regard.”
The Welsh government accepted the information might become less commercially sensitive over time.
Dr Lucy Budd, an air transport management expert at Loughborough University, said a marketing deal of this nature was not unusual.
“There are many examples of urban, regional and national tourist boards partnering airports to support new routes and promote the attributes and attractions of the destination in question,” she said.
She said a similar deal was set up on an EasyJet route between London Gatwick and Gothenburg.
Mr Davies said everyone wanted Qatar Airlines to be a success, but “the gap between rhetoric and reality where the Welsh government is concerned usually ends up with the taxpayer footing a significant bill”.
Plaid Cymru AM Rhun ap Iorwerth said the commercial sensitivity argument did not stack up, adding: “We need to be sure that Wales is getting a good deal here, too.”
UKIP’s Welsh assembly leader Caroline Jones said, following “the Pinewood debacle”, the public and the assembly should be allowed to scrutinise the deal.
“Are the Welsh taxpayer paying through the nose to enhance Qatar Airways’ profits? Without transparency we won’t know until it’s too late,” she added.
A spokeswoman said the Welsh government strived “to be as open and transparent as possible”.
“However, we have a duty to the companies we work with to protect the confidential nature of any business agreements,” she said.
The marketing partnership had been widely welcomed as increasing Wales’ profile, she added.
“Commercial partnerships are an important part of Visit Wales’ marketing work which generated an additional value of £356m to the Welsh economy in 2017.”