Her conservative CDU/CSU alliance has won 32.5% of the vote, remaining the largest party in Germany's parliament, according to the ARD poll.
Its coalition partner, the social democratic SPD, has gained 20%. Meanwhile, the AfD, a far-right nationalist, anti-Islam party, was on track to win 13.5%, emerging as Germany's third-strongest party.
Those numbers mean that the SPD, led by Martin Schulz, has fallen to a new post-World War Two low.
The party's deputy leader, Manuela Schwesig, said the result was a heavy defeat that meant the party would go into opposition, putting an end to the current coalition with Mrs Merkel.
AfD's performance, better than what opinion polls had forecast, means that the far-right party will have a seat at the Bundestag for the first time.
Mrs Merkel will now have to search for new coalition partners - a process that could take months.