In a partial recount of 4,753 ballot boxes, the conservative Hernandez won 50.1 percent of the votes, against some 31.5 percent for his rival Salvador Nasralla.
Honduras' electoral tribunal said on Sunday that a partial recount of votes from the disputed presidential election showed broadly the same result as previously, giving the lead to current President Juan Orlando Hernandez.
In the partial recount of 4,753 ballot boxes, the conservative Hernandez won 50.1 percent of the votes, against some 31.5 percent for his rival Salvador Nasralla from the center-left coalition Opposition Alliance against the Dictatorship.
The tribunal did not specify exactly how many votes from the November 26 election were recounted. There are some 18,000 ballot boxes overall.
Including all votes, Nasralla trails conservative Orlando Hernandez by 1.6 percentage points according to the official count, which has been questioned by the two main opposition parties and a wide swathe of the diplomatic corps.
Observers from the Organization of American States (OAS) issued a series of recommendations this week to authorities including a recount of disputed ballots.
"What we can say is that the results of the recount are extremely consistent with what we had originally," David Matamoros, president of the Supreme Electoral Tribunal (TSE) said.
The election has been plagued with problems since voting stations closed, sparking concerns of deepening political instability in the poor, violent Central American nation.
The tribunal declared Nasralla the leader in an announcement on the morning after the vote, with just over half of the ballot boxes counted. However, it gave no further updates for about 36 hours. Once results then started flowing again, Nasralla's lead quickly started narrowing, sparking a major outcry.
Since early December, the government imposed a curfew which is still in place in 5 of the country's 18 departments.
Opposition parties on Friday presented formal requests to annul the election.
On Sunday afternoon, opposition groups were expected to take to the streets to protest the results. The electoral tribunal has until December 26 to declare a winner.