The head of the union, which has 2.4 million members in the metalworking industry, said in an interview that he would not be urging a vote for the SPD as IG Metall did in 2005 for former chancellor Gerhard Schröder.
"I know that relations between the SPD and the union have historically been very strong, but we are now in the 21st century. The time when the unions can say 'vote for this person or that person' is over," Berthold Huber told daily Süddeutsche Zeitung.
"People can think for themselves," he added.
Huber's comments represent the latest setback in what has been a very challenging week for SPD leader Frank-Walter Steinmeier, who is seeking to topple Merkel in September 27 elections.
Steinmeier, foreign minister in Germany's governing coalition, has seen his party lag more than 15 points behind Merkel's conservatives in the polls, while his personal popularity is 37 points behind the high-flying chancellor.
Steinmeier also lost a key ally to a political scandal this week when Health Minister Ulla Schmidt was forced to pull out of his campaign team after she took her official car with her on holiday at public expense, prompting a public outcry.