The Galatasaray midfielder is a major doubt for the Oranje's game against Romania on March 22, though the former Bayern Munich boss could at least be pleased with the 3-0 result.
The Galatasaray midfielder went off in the 36th minute in the 3-0 victory at the Amsterdam ArenA for Rafael van der Vaart, who went on to open the scoring early in the second half.
Goals from Robin van Persie and Ruben Schaken wrapped up the win for the Oranje, but Sneijder's injury cast a slight shadow over the Group D battle and he now seems set to be absent for the Romania match next week.
Van Gaal told reporters: "We have to wait and see. We must look at the reaction of his groin tomorrow and the day after.
"If you ask for a substitution after half an hour, I don't think you've got a big chance to play on Tuesday."
Daryl Janmaat's low pass for Van der Vaart enabled the Hamburg midfielder to break the deadlock, and Van Gaal was pleased his side had a fruitful final 45 minutes after a frustrating first half.
"It was a sharp pass, and then we had a little luck and we were able to turn the game with it,'' he said. "There wasn't much time. The first half was an improvement in the second half.''
Netherlands tops Group D with five wins from five games, with Hungary above Romania in second spot on goal difference on 10 points.