The Il-96 jet brought home 46 Russian diplomats and their family members reported the Russian news agency TASS.
A second plane carrying rest of the Russian diplomats is expected to arrive later on Sunday.
The countries including Russia, US, UK, Germany along with the European Union have been engaging in a diplomatic war over the poisoning case.
On March 23 the United States expelled 60 Russian intelligence and diplomatic officers residing in New York and Washington D.C. in response to Russia for allegedly poisoning ex-Russian spy Sergei Skripal and his daughter Yulia Skripal who were found slumped on a bench at a Salisbury park in the United Kingdom on March 4.
Later the Russian embassy to the US launched a Twitter poll asking users to vote on which American consulate should be closed in Russia. The US has an embassy in Moscow and consulates in St. Petersburg, Yekaterinburg and Vladivostok, The Guardian reported.
Earlier on March 31, Russia expelled 59 diplomats from 23 countries including Canada, Poland, Germany, Lithuania, Czech Republic and Moldova.
Later Russia asked more than 50 UK diplomats to leave the country on the same issue in retaliation for the suspension of 21 Russian diplomats last week. (ANI)