"They'll be there. I would think that Ryan may be would not be there, maybe he will be in a different position", he said and exuded confidence that he would win the November 8 general election against Democratic rival Hillary Clinton.
Mr Ryan, the vice presidential candidate in 2012, pulled his support after the billionaire's snarling performance in the second presidential TV debate s and the release of tapes revealing Trump's lewd and sexist comments on women.
He continued: "Disloyal [Republicans] are far more hard than Crooked Hillary".
He particularly singled out House Speaker Paul Ryan, who told Republicans on Monday he would no longer campaign for Mr Trump with four weeks to go until election day. He later said in an interview with Fox News host Bill O'Reilly he neither wanted nor needed Ryan's support.
Oklahoma Republican Jim Bridenstine, a member of the conservative House Freedom Caucus, tweeted on Wednesday that he will not support Ryan - presumably, for speaker in the next Congress - because of Ryan's failure to defend Trump.
Sens. Chuck Grassley and Joni Ernst, both Iowa Republicans, have publicly condemned Trump's remarks but said they still plan to vote for him.
"I'm certainly not going to vote for Hillary Clinton", Thune said. Campaign manager Kellyanne Conway said GOP leaders were being "wishy-washy" and "pussyfooting" around, rather than coming out in unanimous support of Trump.
"First of all, I want to make it very clear that the RNC is in full coordination with the Trump campaign, and we have a great relationship with them".
Trump also tweeted Tuesday that the "shackles have been taken off me and I can now fight for America the way I want to".
At least 40 Republican senators and congressmen have revoked their support for the embattled Republican nominee - with almost 30 urging him to quit the race altogether. While the Democrats might disagree individually, they have rallied around Hillary Clinton, exemplifying the adage "party trumps person".
Democrats had already felt bullish on their prospects for flipping the Senate, but the Trump tape's fallout has potentially put more suburban House districts now held by Republicans in play.
"The very foul mouthed Senator John McCain begged for my support during his primary (I gave, he won), then dropped me over locker room remarks", he said about the party's 2008 presidential candidate who is seeking re-election to the Senate from Arizona.
She said she would not continue to call for Trump to step aside.
"He has a lot of work to do, I think, to win this election", Thune told the newspaper.