The Argentina captain had said that rumours of him moving clubs at the weekend were "lies".
But the 27-year-old said "nobody knows what the future holds" at Monday's Ballon d'Or ceremony in Zurich.
He lost out to Real Madrid's Cristiano Ronaldo as world footballer of the year for the second year in a row.
Messi was asked if he thought he would end his career at Barcelona.
"I'm not sure what's going to happen," he said.
"I don't know where I'll be next year although I've always said I want to end my career at Barcelona."
It had been suggested La Liga's record goalscorer might leave the club following reports of a training-ground row with manager Luis Enrique, who took over last summer.
He has spent his entire career at the Nou Camp, winning three Champions Leagues and six La Liga titles as well as four world footballer of the year awards, since making his debut in 2004. He is contracted until 2019.
After scoring in Sunday's 3-1 victory over Atletico Madrid, Messi said: "I have no intentions of leaving for any team, not Chelsea nor Manchester City.
"I'm tired of all the things that people have been saying."

Alun Ffred Jones said Natural Resources Wales (NRW) had offered confusing advice and was sometimes seen as being "too close" to the Welsh government.
Mr Jones has outlined his concerns in a letter to NRW, following an inquiry.
But NRW said it was "clear" about its purpose and insisted it was already dealing with many of the points raised.
The body was formed in 2013 by merging the Countryside Council for Wales, the Environment Agency and the Forestry Commission.
In his letter, Mr Jones wrote: "NRW does not appear to be clear about its purpose as an organisation... many of the more specific issues raised... stem from the confusion that exists within NRW about its purpose and the apparent lack of awareness at the top of NRW of how it is perceived on the ground by key stakeholders and staff."
The letter states some councils were confused on occasions when NRW stated it had no objection to a planning development, but then listed "serious concerns" about its impact.
Mr Jones added some organisations raised concerns the environment body was too close to Welsh ministers, particularly in relation to the controversial Â£325m Circuit of Wales race-track project planned in Blaenau Gwent.
NRW chief executive Emyr Roberts said creating NRW had been "uniquely complex" and "nothing like this has ever been attempted before anywhere in the world".
"We are clear about our purpose and working with staff and stakeholders around this new concept of managing our natural resources in a more joined up way," he said.
"We are already taking action on many of the points raised and, against a backdrop of significant change, I'm very proud of the fantastic work our staff have continued to do for the people, environment and economy of Wales," Dr Roberts added.
A staff survey published in April found only 14% of workers at NRW felt the merger that led to its creation was well managed and one in five thought the organisation was well managed.
Just over half of its 2,000 staff took part in the survey.
Barcelona forward Lionel Messi says "I don't know where I'll be next year," but he says he does want to stay at the La Liga club.
[NEXT_CONCEPT]
Wales' environment body is not clear of its own purpose, the chair of the assembly's environment committee has claimed.