Relatives of Emmanuel and Miriam Riva, who are survived by their two teenage daughters, said the couple in their 50s had been celebrating their wedding anniversary in the Belgian capital.
Israeli and Belgian officials also attended the funeral.
"This crime is the result of a hike in anti-semitism in Europe," Internal Security Minister Yitzhak Aharonovitch said in a speech, praising the "important contribution of the couple to the state."
The attack, in which a gunman opened fire at the museum in Brussels on Saturday, killed three people, including the Rivas.
Contacted by AFP, the Israeli defence ministry denied the couple had been in their employ, while the prime minister's office declined to comment on the report.
Belgian investigators yesterday said they were considering a possible terrorist link to the shooting, which also killed a French woman and left a fourth person, a Belgian national, brain dead.
"This is a day of mourning for both our countries, which we share," said Belgian ambassador John Cornet d'Elzius.
Haaretz said Emmanuel Riva had worked in the finance ministry as well as at an organisation called Nativ which was founded in the 1950s to covertly encourage Jewish education in the Soviet Union during the Cold War, and to drive immigration to Israel.
Since the fall of the Iron Curtain, it has been focused on encouraging immigration to Israel among Russian-speaking Jews living in western Europe, particularly in Germany.
"Both were accountants who were employed separately by government bodies," Haaretz said, describing their tools as "numbers and computers, not cloaks and daggers."
Miriam Riva worked for an unspecified "government agency," the paper said.
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