The port of Tallinn said on Wednesday that it shipped 1.641 million metric tonnes (mt) of oil product in September, down 5.8% from August.
The September figure represented a 20% improvement from the same month last year.
But Tallinn's oil product exports, which are mostly made up of Russian fuel oil, have dropped by 12.1% in the first nine months of 2008.
Tallinn handled 15.273 million mt of oil products in the first nine months of 2008 compared to 17.38 million mt for the same period of 2007, according to the port's data.
Russia used to export around 25 million mt of fuel oil a year via Tallinn, as well as light products, according to Reuters.
Following a diplomatic dispute between Russia and Estonia in April 2007, Russian railways began to divert most of the light products to its own ports.
Estonia believes it is only a question of time before Russia also begins to divert more of its heavy fuel oil shipments to its own ports in the Baltic, principally to Ust Luga port.
Estonian Railways Chairman Kaido Simmermann told Reuters last month that he expected there would be no Russian oil shipments through Estonia within three or four years.
Ust Luga would probably be ready to handle heavy fuel oil shipments coming from the Kirishi refinery "at the beginning of next year or in the middle of next year," he said.
Russian oil products make up a large share of Tallinn's cargo throughput.
Tallinn handled a total of 21.87 million of cargo in the first nine months of 2008, a 23.7% drop compared to the same period of 2007.
Simmermann told Reuters that Estonia had been expecting Russia's gradual shift to exporting its energy products through its own ports, but said last years diplomatic clash had accelerated developments.
He said Estonia would focus on shipping non-strategic cargoes for Russia in the future, including container traffic.