The EU has announced a memorial service for July 1st for Kohl, widely regarded as the father of German reunification after the fall of the Berlin Wall and a key figure in European integration.
He died on Friday aged 87.
Maike Kohl-Richter, the former chancellor's second wife, wanted only foreign dignitaries to speak during the ceremony, according to the weekly magazine Spiegel.
Among them is Hungarian Prime Minister Viktor Orban, one of the last public figures to hold talks with Kohl, and who is a strident critic of Merkel's refugee policy.
Kohl-Richter relented only after being warned against creating a scandal, Spiegel said.
Merkel started her political career as a protege of Kohl but later broke with him when he became mired in a party slush fund scandal.
It also emerged that Kohl would not be laid to rest in the family plot of Ludwigshafen, where his first wife Hannelore - who committed suicide in 2001 - is buried.
Bild's former editor-in-chief Kai Diekmann, who is close to the family, told Germany's DPA news agency that Kohl had made the decision to be buried instead in Speyer "in 2015 together with his wife when his health condition was at a critical state".
Kohl had been estranged from his two sons, both from his marriage with Hannelore.
Walter Kohl, who like his brother Peter had not had contact with Kohl for years, said he had learnt of his father's death only through the radio.
In a book published in 2011, Walter described a father who was all-powerful but absent in their lives.
Alongside Merkel, French President Emmanuel Macron and former US president Bill Clinton will address a ceremony in Strasbourg, the EU announced Wednesday.
"The casket holding the remains of Dr Kohl will lie in state covered by a European flag" in the ceremony in Strasbourg, the home of the European Parliament, the statement said.
The European Council, which represents member states, confirmed in a statement that speakers would include Merkel, Macron and Clinton.
Clinton's time in office overlapped with Kohl's in the 1990s when a reunified Germany led efforts to expand the EU and NATO.
European Council chief Donald Tusk, European Commission head Jean-Claude Juncker and European Parliament President Antonio Tajani will also make speeches.
"Following the European Ceremony of Honour, which is expected to last for around two hours, the casket will be brought to Germany, where the former Chancellor will be buried after a funeral service in the cathedral in Speyer," a town further up the Rhine river from Strasbourg, it said.