Finance inister Basil Rajapaksa, the younger brother of president Gotabaya Rajapaksa, had lifted the ban on Tuesday.
The president had earlier touted the policy, including on the international stage, as helping Sri Lankan agriculture become "100-percent organic".
In a briefing to reporters in Colombo, secretary to the ministry of agriculture, Udith Jayasinghe, said there had actually been "no change in the government policy shift to organic fertiliser".
"Some plant nutrients rich in nitrogen will be allowed under strict licensing."
Urea fertiliser, which will remain banned, is widely used in the $1.25 billion tea industry -- the country's biggest export -- as well as in the farming of rice, the staple food.
Jayasinghe said farmers would have to use organic substitutes.
Sri Lanka is among the world's largest exporters of tea. Ceylon tea is valued for its high quality and flavour.
A report by a group of experts warned last month of substantial crop losses and food shortages unless chemical fertiliser was provided urgently.
A member of a presidential committee that studied the transition from chemical to organic fertiliser, Herman Gunaratne, said the sudden shift could have catastrophic consequences, especially for tea.
"We risk losing our international markets for tea," Gunaratne told AFP.
Tea plantation executive Sanath Gurunada told AFP over the weekend that the shortages would be felt fully by October.
"For the moment we have stocks (of fertiliser), but it would run out in about a month or two. After that we will not get the crop that we used to harvest," he told AFP at his Hidellana tea factory in the country's south.
"With a decline in crop, our foreign exchange earnings will also go down."