German officials said their visit to the "Bronze Age of Europe -- Europe Without Borders" exhibition at the Hermitage museum had been scrapped due to what German media described as a wrangle over the future of the so-called trophy art.
Merkel was reported to be keen to express her view that the treasures belonged in Germany, and to have ditched her speech and the entire visit, when this hit opposition in the Russian camp.
But despite his spokeswoman saying that Putin was not planning to go anyway, just a few hours later he performed what seemed like a U-turn and said both he and Merkel would be there.
"In the evening we are visiting the exhibition at the Hermitage. We had not cancelled anything, we just wanted to see if we would have enough time," Putin said at a news conference in Saint Petersburg alongside Merkel.
Merkel added: "We have agreed to go to the Hermitage. It is an important exhibition."
Earlier in the afternoon, Germany's deputy government spokesman Georg Streiter answered a question about what had been planned for her speech by saying that she may have pointed to the "view supported by international law" that the art works should be handed back to Germany.
Nearly 70 years after the end of the war, disputes over war booty remain as Germany seeks the return of treasures looted by the victorious Red Army and talks between the two countries on the issue continue.
Merkel was in the Russian city Friday for an International Economic Forum as well as bilateral talks and a dinner with Putin, and the exhibition opening was slated for later in the day.
Streiter said there was "no clash" and that the event was struck from the programme "by mutual agreement" after Putin announced a scheduling problem. "President Putin apparently time-wise had no opportunity for an opening event at which there are also speeches," Streiter told a regular news briefing.
"This exhibition and its particular background would have required a presentation via an opening speech," Streiter said, adding it would not have been "appropriate" for an inauguration that raced through the exhibition.
Earlier in Moscow Putin's spokesman denied that he had ever planned to visit the exhibition at the Hermitage. "The exhibit will indeed open but there have never been any precise plans to visit it," Dmitry Peskov told AFP.
"Putin will not go, no, he has never had any plans to."
Yet this, and any scheduling problems were seemingly solved within hours.
The "Bronze Age of Europe -- Europe Without Borders" exhibition includes about 600 items brought after the war from Germany to Russia and has been organised through cooperation between German and Russian museums.
In the 1950s, after the death of Stalin, the Kremlin authorised the return to Germany of 1.5 million works of art, including the celebrated Pergamon Altar, built in the second century BCE and now one of Berlin's top tourist attractions.
But further negotiations have proven difficult.
Merkel and Putin clashed earlier in the year over a crackdown by Moscow on non-governmental organisations while the European Union and Russia have persistent differences over the slaughter in Syria.