Somaliland declared its independence in 1991 but is not recognised by the international community, which considers it an autonomous region of Somalia.
The foreign ministry said in a statement on Thursday that government had cut all diplomatic ties after Guinea “accorded the protocol of head of state… to the leader of a separatist movement”.
The statement accused Guinea of “disregarding callously all the relevant resolutions of the UN and African consensus”.
Somaliland President Muse Bihi and his delegation reportedly met officials in Guinea to discuss establishing a formal relationship.
The Somaliland government has made no official statement about the visit so far.
Formerly a British protectorate, Somaliland merged with former Italian Somaliland in 1960 to create Somalia.
But it seceded and declared itself independent in 1991 as Somalia plunged into chaos after the fall of autocrat Siad Barre.
Somaliland has been pushing for independence ever since.
It has its own government based in the self-appointed capital of Hargeisa, its own army and prints its own currency.
It is also considered much more stable than the rest of Somalia, which is plagued by clan disputes, corruption and a violent insurgency waged by the Al-Shabaab militant group.
“Guinea had violated the sovereignty of Somalia and the unity of its people,” Somalia Foreign Affairs Minister Ahmed Ise Awad said in a news conference.
“The federal government of Somalia and its people will not tolerate violations against their sovereignty, unity and independence,” he added.