The letter asked Zuckerberg to answer five questions about the "Trending" feature, including whether Facebook keeps a record of curators' decisions to include or exclude stories and how many pieces related to conservatives have been rejected.
Additionally, Thune asked for a briefing for committee staff on the "Trending" feature.
The former curator's claims, reported Monday by Gizmodo, have caused an uproar on the political right. "It is beyond disturbing to learn that this power is being used to silence view points and stories that don't fit someone else's agenda," the Republican National Committee wrote Monday in a blog post.
Facebook Vice President for Search Tom Stocky said the claims are false.
"Facebook is a platform for people and perspectives from across the political spectrum," Stocky wrote Monday in a Facebook post.
"There are rigorous guidelines in place for the review team to ensure consistency and neutrality. These guidelines do not permit the suppression of political perspectives. Nor do they permit the prioritization of one viewpoint over another or one news outlet over another . . . We do not insert stories artificially into trending topics, and do not instruct our reviewers to do so."
A spokesman for Senate Minority Leader Harry Reid, D-Nev., slammed Thune for launching the probe.
"The Republican Senate refuses to hold hearings on Judge Garland, refuses to fund the President's request for Zika aid and takes the most days off of any Senate since 1956, but thinks Facebook hearings are a matter of urgent national interest," Adam Jentleson wrote in an email.
"The taxpayers who pay Republican senators' salaries probably want their money back."