There is no Israeli military presence in Somaliland and there are no talks about establishing a military base there, he told "Reuters" Somaliland's Defense Minister Mohamed Yusuf Ali.
Speaking on the sidelines of a business conference in Tel Aviv, he said Israel was training Somaliland's military and police forces, but dismissed claims of talks over an Israeli military base as "rumors".
Israeli Ambassador to Somaliland Michael Lotem declined to comment.
Strategically located in the Horn of Africa, Somaliland has enjoyed de facto autonomy and relative stability since 1991, after seceding from Somalia during a civil war.
Israel recognized Somaliland as an independent state in December, becoming the first country to do so. Somalia rejected the decision, calling it a "deliberate attack" against its sovereignty.
In February, Somaliland President Abdirahman Mohamed Abdullahi told Reuters that while future military cooperation with Israel was being discussed, the establishment of Israeli military bases was not a topic of discussion.
On Sunday, the "Somali Guardian" newspaper reported that Israel had established an intelligence base in Somaliland and that options for a future military base were being discussed, but these claims were not officially confirmed.