Rasmussen was to arrive in Yerevan to meet Armenian President Serzh Sargsyan. In a statement from his Twitter account, the secretary-general said his plane returned Wednesday to Brussels because of technical reasons.
"Despite the delay, I am looking forward to visit(ing) the Caucasus Thursday and Friday," the message stated.
Rasmussen is to meet Thursday with Foreign Minister Edward Nalbandian and Defense Minister Seyran Ohanyan.
His scheduled arrival follows concerns that a decision by Azerbaijan to pardon a military official accused of killing an Armenian counterpart in Budapest could reignite regional tensions.
Azeri officer Ramil Safarov was serving a life term in prison for the death of an Armenian soldier Gurgen Makarian in 2004. Both men were in the country taking English-language courses established there by NATO.
The Organization of Security and Cooperation in Europe expressed "deep concern" over the pardon. Safarov received a hero's welcome upon his return to Azerbaijan, getting a promotion in rank and pay lost since his arrest.
Skirmishes broke out between Azeri and Armenian forces in June over the disputed territory of Nagorno-Karabakh. Both sides have gone to war over the territory, which is recognized as part of Azerbaijan.