The protocol concerned the land-based part of the transit leg of the TurkStream gas pipeline, which Gazprom said meant that work to implement it could now begin.
Turkey had delayed issuing a permit for the Russian company to start building the land-based parts of the pipeline which, if completed, would allow Moscow to reduce its reliance on Ukraine as a transit route for its gas supplies to Europe.
A source said in February the permit problem might be related to talks between Gazprom and Botas about a possible discount for Russian gas.
Turkish President Tayyip Erdogan said earlier on Saturday Turkey and Russia had reached a retroactive agreement for a 10.25 percent discount on the natural gas Ankara buys from Moscow.
Gazprom said in the Saturday statement, without elaborating, that the dispute with Botas would be settled out of court.
*Vladimir Soldatkin & Oksana Kobzeva; Maria Kiselyova – Reuters