Matthias Mueller told the BBC that VW was still in "constructive dialogue" with regulators and hoped the firm would be "judged fairly". Mueller also said he was postponing the company's year-end financial results and the AGM.
He also warned that the €6.7bn (£5.2bn) set aside to cover the costs of the scandal, which was one of the biggest corporate stories of last year, might not be enough.
Mueller was speaking at the Geneva Motor Show, where the German car manufacturer was launching its electric-powered city cars, e-up!.
A protester, initially reported to be British comedian Simon Brodkin, who previously gatecrashed a FIFA press conference and showered then president Sepp Blatter with banknotes, attempted to fit a 'cheat box' device on to one of the new cars.
Ed Coke, director at Reputation Institute, said: "Volkswagen has a long journey ahead of it to reputational recovery. There was a tremendous amount at stake for the company when the emissions scandal broke in September, and we would only expect very limited progress to its reputational recovery six months on.
"This recent regulatory and legal setback, alongside Simon Brodkin gatecrashing the Geneva Motor Show, reinforces the magnitude of the situation, and the lack of resolution of the issue.
"Our data shows that VW continues to be inextricably linked to the defeat device scandal, and the company will need to work hard to identify not only what it needs to do, but how it needs to communicate its recovery for some years to come."
