Former WDA chief economist Brian Morgan questioned the assembly government's ability to deal with the bodies.
Ieuan Wyn Jones asked whether his Economic Development Minister's attack on the WDA was cleared with him.
BBC: No war on England, the First Minister declared this week.
The Welsh government said its new way of attracting investment was "flexible", while the WDA had run its course.
BBC: Wales needs to be united to win investment, says CBI Wales
The WDA, which owns the unit, said it had agreed to lease the unit to the dentist providing he received planning permission.
BBC: NEWS | UK | Wales | Mid | Dentist plans surgery in WDA unit
The investment has been supported by the Welsh Assembly Government with a regional selective assistance grant and also by the Welsh Development Agency (WDA).
The functions of the WDA were later taken over by the Welsh government, who sold the site to the builder Taylor Wimpey North West.
He described Friday's meeting as "constructive" and said the company would work with the Assembly and the WDA to try to keep the plant open.
As he emerged from the meeting, Mr German said the assembly and the WDA would be working together to try and win fresh orders for the company.
"The county council and WDA have agreed to part fund a feasibility study into a new centre and that will now go out to tender, " said Mr Morgan.
"Our new model is a more flexible and responsive model and fit for the future, not simply a throw-back to the WDA, which had run its course, " said a spokesperson.
BBC: Wales needs to be united to win investment, says CBI Wales
Those defences - a flood bund, or mound - had been put in place as part of original outline planning permission granted to the Welsh Development Agency (WDA) by Denbighshire council.
Information technology consultants ITEC - who work closely with the WDA, Business Connect and West Wales TEC - are also in talks with Cyberpub about training courses in pubs during quieter periods.
He praised the performance of the WDA, and said staff had achieved "minor miracles" to overcome the problem which meant investors had to go to both it and the assembly government for grant help.
Had that forward planning been done, said Mr Colman, then the public bodies funding the set up of the garden - namely the Welsh assembly government, the Wales Tourist Board and the WDA - "might have deduced" that they would soon be asked for extra cash.
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