Sir Keir Starmer, the party’s shadow Brexit spokesperson, said “nobody was ruling out” the option.
It came hours after shadow chancellor John McDonnell announced the only choices should be on the “nature” of a deal with Brussels.
Emotional splits have emerged within Labour as it grapples with pressure to campaign for a “people’s vote” on any negotiated settlement.
Kicking off Labour’s annual conference in Liverpool on Monday, Mr McDonnell said any new referendum on Brexit should “respect” the 2016 result to leave.
Asked by Sky News if the question to Leave or Remain should be revisited in a potential future vote, Mr McDonnell said: “No – I think it’ll be on the deal itself.
“If we’re saying we respect the referendum, it’ll be about the nature of the deal that the prime minister brings back or the one that we can negotiate.”
Mr McDonnell was confident Labour could negotiate a good deal with Brussels by 29 March 2019, the date when Article 50 runs out and Britain leaves the European Union.
The EU has suggested December is the cut-off date for negotiations, to allow enough time for a deal to be voted on by the 27 other countries’ parliaments.
Asked if Labour could negotiate a deal in six months, Mr McDonnell said: “We think we can, we think we can negotiate a deal.”
But he was contradicted that afternoon by Sir Keir.
“We weren’t ruling options and nobody was ruling out Remain,” he told journalists.
Sir Keir did not respond to questions about whether Mr McDonnell was wrong.
Labour MP David Lammy warned a choice without Remain on the ballot paper would amount to a “farcical referendum on no deal or a bad deal”.
“It absolutely must include the right to remain in the EU,” he added.
It came hours after Labour averted some members’ calls for committing to campaigning for a referendum on the final Brexit deal.
The party will prioritise getting a general election, but if unsuccessful will “support all options remaining on the table, including campaigning for a public vote”.
Leader Jeremy Corbyn said on Sunday he would be “bound” by a vote at Labour conference on whether the party should campaign for another referendum.