Russia's oil export flows have been disrupted since April, when high levels of organic chloride were found in crude pumped via the Druzhba pipeline to Ust-Luga and other European countries.
Six tankers with 598,000 tonnes of tainted oil were loaded at Ust-Luga, Kazakh Deputy Energy and Mineral Resources Minister Aset Magaulov told Reuters.
"First, companies that sold the oil will talk to buyers about a discount, then ... (Kazakh pipeline operator) Kaztransoil will have separate talks with Transneft," Magaulov said.
Neither Transneft nor the Russian energy ministry replied to a Reuters request for comment.
Magaulov added that two separate tankers with 199,000 tonnes of clean Kazakh oil were loaded from Ust-Luga between May 10 and May 15. Russia's energy ministry said earlier that clean oil had started to be loaded at Ust-Luga.
Russian Deputy Prime Minister Dmitry Kozak said on Thursday that Transneft would compensate all parties for losses incurred from contaminated oil if they could prove the damage, while the first European refinery declared force majeure.
"Based on the oil agreement with Transneft, given the fact that we supplied clean oil but it got contaminated ... there should be compensation from Transneft," Magaulov said.
Kazakhstan, which produces around 1.8 million barrels per day (bpd) of oil, is the second-biggest oil producer among former Soviet countries after Russia. Kazakhstan exports around 12 percent of its oil via Russia's Ust-Luga.
Magaulov said a preliminary agreement had been reached with buyers under which they would take the contaminated oil at a discount. However, talks on such a discount are continuing and there is no estimate of potential compensation.
ExxonMobil, Chevron, Eni, CNPC and Lukoil are among the international companies producing oil in Kazakhstan.
The Druzhba pipeline splits in Belarus into a northern spur to Poland and Germany and a southern leg via Ukraine to Slovakia, Hungary and the Czech Republic. Only Hungary has resumed test flows to see whether its refinery equipment can withstand the contaminated oil.
Druzhba can pump 1 million bpd, or 1 percent of global oil demand. Ukraine and Belarus have said they will ask Transneft for compensation.
On Thursday, Russia's Kozak said it would take 22 days to clean one branch of Druzhba and seven days for the other, without specifying which was which.
Meanwhile, Poland has increased seaborne oil imports and Czech refiner Unipetrol will start drawing the second batch of an emergency loan of crude from state reserves overnight.
France's Total has suspended operations at some units of its 230,000-bpd Leuna refinery in Germany for technical checks following the Russian contamination.
Total said it was trying to manage any long-term supply complications and planned to resume operations on Saturday using crude sent via the Polish port of Gdansk.
Russian oil production remained under pressure due to the pipeline debacle. Output from May 1-16 fell to 11.156 million bpd, below the 11.18 million bpd level set in a supply-limiting deal with producer group OPEC, two industry sources said.
Before the contamination, sources indicated Moscow wanted to pump more from July along with the Organization of the Petroleum Exporting Countries, which was considering whether to raise output if Venezuelan and Iranian supply dropped further.
A panel of OPEC and non-OPEC ministers meets on Sunday in Saudi Arabia to discuss the market and make recommendations. The group, known as OPEC+, gathers in June to decide whether to renew the supply-cutting deal.
(Reporting by Mariya Gordeyeva in NUR-SULTAN and Alla Afanasyeva in MOSCOW; Additional reporting by Jan Lopatka in PRAGUE; Gleb Gorodyankin and Olesya Astakhova in MOSCOW; Bate Felix in PARIS; Writing by Katya Golubkova; Editing by Dale Hudson)
By Mariya Gordeyeva and Alla Afanasyeva