Mr Juncker accused Switzerland of not keeping its promises amid the ongoing framework agreement and stock market access negotiations.
The Commission President said the institutional framework agreement “had been repeatedly promised” but had still “not been achieved”.
Brussels has been increasing the pressure on Switzerland to agree on a new treaty with the European Union.
Switzerland is not a member of the EU but maintains single market access through its membership of the European Free Trade Agreement.
Fears have grown the EU is attempting to use trade talks with Bern to strengthen Brussels Brexit negotiating with Britain.
The proposed new treaty between the EU and Switzerland would replace the currency bilateral accords that govern the country’s ties with Brussels.
Mr Juncker was presented with a question on the stalled talks during a press conference in Brussels on Wednesday.
He responded: “I have met with former Swiss president Doris Leuthard eight times since coming to office and have always indicated that an institutional framework accord is necessary.
“It was promised on many occasions but this has not materialised.
“I remain, despite that, a friend of Switzerland – although I have always noticed on holidays that when I met Swiss people, they have dim view of me.
“I think the Swiss Government and the Swiss media have projected an image of me that in no way corresponds the reality.”
Last week, Swiss finance minister Ueli Maurer cast doubt on whether a framework will be even possible between Bern and Brussels.
He said: “For several years, Switzerland has promised that a framework agreement will be reached with the EU.
“But such a domestic policy is increasingly unlikely. We have never corrected the impression towards the EU that a framework agreement in Switzerland increasingly meets with rejection.
“When the EU puts pressure on us, at least half of this is due to such omissions. A framework agreement is not possible in the foreseeable future.
“If we try anyway, both parties will come under pressure and there will be no good bargaining results.
“We should not try to negotiate before Brexit. We are not that fast. This does not match our mentality.”