The alliance of the Christian Democratic Union (CDU) and Christian Social Union (CSU) has been overtaken by the Greens. The party led by Ms Merkel for 18 years has seen its approval rating drop by 12 points in the last four months.
A YouGov survey of more than 1,600 registered voters found just 24 percent of Germans would vote for the CDU/CSU alliance if an election was held next Sunday.
The union had been polling at highs of 36 percent in January.
The German Chancellor is under increased scrutiny over her handling of the coronavirus pandemic.
Much of Germany has been in lockdown since the start of the year as a third wave of infections grips Europe.
The poll suggested the Greens are now the most popular party in Germany.
Alliance 90/The Greens, more commonly known as Greens, are currently polling at 25 percent – one point ahead of the union.
The surge represents a seven percent increase from where the party was in January and February.
The Social Democratic Party of Germany – the junior partner in the ruling coalition – is also shedding support.
Annalena Baerbock is set to be the Greens’ candidate for Chancellor – the first time the party has been in the race for the top job in its 40-year history
Germany’s Vice Chancellor Olaf Scholz is to enter the running for his centre-left Social Democrats.
The YouGov poll asked 1,643 registered voters from April 23-26.
(Additional reporting by Monika Pallenberg)