Andrew Peek has been placed on administrative leave pending the inquiry, Axios reported.
He is the third head of European and Russian affairs at the National Security Council to leave the post in the past year.
It was not immediately clear what the reported security investigation involved.
Bloomberg reported that he had been escorted from the White House, quoting three sources speaking anonymously.
Mr Peek, who previously worked as an expert on Iran and Iraq and acted as a national security adviser to Republican senators Gordon Smith and Mike Johanns, took up the post in November.
Mr Trump has taken a dramatically different attitude towards Russia and Vladimir Putin than previous administrations.
He has publicly praised the Russian president, even declaring at a press conference in Helsinki that he took his word over that of US intelligence agencies that Russia did not try to interfere in the 2016 election.
During the campaign he called on Moscow to try to unearth emails deleted by his Democratic opponent, Hillary Clinton, saying: "Russia, if you're listening, I hope you're able to find the 30,000 emails that are missing. I think you will probably be rewarded mightily by our press."
Mr Trump has also held several private meetings with Mr Putin, at one point allegedly forcing an interpreter to tear up their notes of the conversation.
The links between his campaign and Russia led to the Mueller investigation, which concluded that there was no evidence of a concerted co-ordination but did point to efforts at obstruction of the inquiry.
During the impeachment hearings, Mr Morrison testified that there had been a quid pro quo offered by Mr Trump to his Ukrainian counterpart, Volodymyr Zelensky – that the US would release military aid and arrange a White House meeting if Kiev announced investigations into Democratic presidential candidate Joe Biden.
In her testimony, British-born Dr Hill called on politicians to stop peddling "fictional" narratives, favoured by Mr Trump and his supporters, that Ukraine rather than Russia had interfered in the 2016 election. She said that doing so played into the hands of the Russian secret services.
This week Mr Trump’s impeachment trial will begin in the Senate where he is expected to be acquitted by the Republican majority.
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