Botnia and Spain's Ence are building two pulp mills worth a combined $1.7 billion along the Uruguay River, which forms a natural border between Uruguay and Argentina.
The stoppage comes after months of protests by Argentines living near the plants, who fear that run-off from the mills will ruin their waterfront and pollute the air.
"The Uruguay government has said that in this (90-day) period of time, both countries will analyze the environmental impact of the projects in the region," Botnia said in a statement.
The dispute has generated diplomatic friction. Uruguayan President Tabare Vazquez promised this month to ask the companies to temporarily suspend construction if Buenos Aires would persuade protesters to call off crippling blockades of a main highway leading into Uruguay from Argentina.
The blockades were lifted last week.
Argentine President Nestor Kirchner and Uruguay's Vazquez plan to meet on Wednesday to discuss the next steps.
Ence has said it is willing to cooperate with the Uruguayan government, but it was not clear whether it would suspend construction.
Uruguay defends the projects as its biggest industrial investment and the two firms have said they are using the most environmentally friendly technology available in the industry, complying with strict European Union standards.