The Federal Council approved his early departure ‘by mutual agreement' at its regular meeting on Wednesday, the defence ministry said in a statement.
Blattmann, 60, has been army chief since 2009. He was not due to retire until the beginning of 2018.
Swiss media have speculated that Blattmann may have been given his marching orders by new defence minister, Guy Parmelin, who took over from Ueli Maurer at the beginning of the year.
“Federal Councillor Guy Parmelin thanks the army chief for his many years of committed and far-sighted service to the army and the defence ministry,” the statement said.
“André Blattmann took over the army when it was going through a difficult phase.”
The Blick newspaper said Parmelin, who like Maurer belongs to the rightwing Swiss People's Party (SVP), was “putting his own stamp” on the ministry.
It said he had also abruptly suspended the Bodluv air defence project initiated by his predecessor.
According to Blick, Blattmann's early departure was being sweetened with a year's salary of 376,000 francs.
Parmelin justified the payment following criticism from the Social Democratic Party (SP), saying it was in line with legal regulations and was not a golden parachute.
Blattmann's resignation comes just after parliament gave the go-ahead to a new reform of the Swiss army.