Joyce narrowly won back the leadership earlier in the week, defeating Michael McCormack in a ballot of the 21-member party room.
Littleproud, long touted as leadership material, scotched reports a succession plan was central to Joyce’s strategy.
“There is no secret deal,” the agriculture minister told the ABC on Wednesday.
“This is nonsense and I don’t intend to engage it. I’ve made public comments about what my position was, and I think my record lives up to that.”
Littleproud declared no one was owed the leadership of the party, making a deal impossible.
There is speculation Mr Littleproud would have contested the leadership ballot if McCormack stood aside.
Instead, he retained his deputy leadership unchallenged.
“It was a traumatic day but democracy has made its call. Now we have to just get on with the job and win the next election under Barnaby,” Littleproud told the Nine Network.
The Nationals leader is thrashing out a new confidential coalition agreement with Prime Minister Scott Morrison.
Climate change and energy policy is expected to feature heavily along with priorities for water, infrastructure and regional development.
Joyce is also weighing up the Nationals’ ministerial roles with Bridget McKenzie expected to return to cabinet at the expense of fellow Victorian Darren Chester.
The deputy prime minister took over his predecessor’s roles in infrastructure, transport and regional development on Tuesday when he was sworn in on Tuesday.
Morrison has been stuck in quarantine at The Lodge while the junior coalition partner switched leaders.
The prime minister urged MPs and senators via video link about the dangers ongoing disunity could cause for the government’s re-election hopes.
Morrison said having a clear plan, staying united and having an ability to “get stuff done” could deliver victory.
“If we fail on those things, we will hand the reins of government to those who are not fit to handle them and we will regret that forever,” he told a joint party room meeting.
“We’ve got to focus. No time for individual agendas or pet projects.”
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