The new hoods were installed on Monday, army secretary Maj Gen Pollapat Wannapaktr said.
But vendors are still forbidden to cook the popular pungent dish, and lower ranks who rate it one of their favourites still have to go outside the building the buy it - to ensure their superiors are not distracted from their vital duties.
The canteen in the Office of the Secretary Building at army headquarters was recently refurbished with a new air conditioning system and cooking hoods installed above each vendor's stall.
But senior bureaucrats in the building complained about the odours from the canteen - especially the smell from cooking pat kaprao (stir fried chicken or pork with garlic, chilli and holy basil). They said they could not do their jobs properly if the dish was being cooked in the building, and suggested lower echelon staff buy it outside.
The issue came to public notice when pictures of notices announcing it was now forbidden to order fresh cooked kaprao in the canteen were posted on social websites.
Army chief Gen Prayuth Chan-ocha was clearly uncomfortable when questioned about the ban, but said traders had already been informed that customers who wanted freshly cooked kaprao would have to buy it somewhere else.
Maj Gen Pollapat said on Monday that the cooking of strong smelling dishes would continue to be prohibited in the headquarters building, depite the installation of the larger hoods in the canteen.