Martin Griffiths told the UN Security Council that there is "no time to lose" in brokering a peace deal to bring the fighting to a close.
"The fragmentation of Yemen is becoming a stronger and more pressing threat," the British diplomat said via videolink from Jordan.
"The stakes are becoming too high for the future of Yemen, the Yemeni people and the wider region. Yemen cannot wait," he added.
Griffiths comments came as Yemeni separatists drove government troops out of two military camps in deadly clashes in Abyan province on Tuesday, reinforcing their presence in the south after they seized the de facto capital Aden.
He condemned the recent takeover of Aden by the Southern Transitional Council (STC) in clashes that reflected the independence ambitions of southern Yemen and left around 40 people dead.
"We certainly cannot underestimate the risks that these events pose for the future of the country," Griffiths told delegates.
"No country can tolerate the stresses of internal conflict indefinitely," he added saying the war must be brought to an end "swiftly and peacefully."
The separatist Southern Transitional Council (STC) and government forces have been fighting the Iran-aligned Huthi rebels in a years-long war that has pushed the country to the brink of famine.
A spike in tensions between the two has constrained their cooperation in the fight against the Houthis, however.
Griffiths warned that further deterioration of the security situation in Aden and other areas could provide fertile ground for a resurgence of al-Qaeda in the Arabian Peninsula and the so-called Islamic State.
"(It) almost certainly will allow those activities to expand and gather momentum once again as we have seen before, with a terrible impact on the civilian population and prospects for future stability in this key strategic location," he said.
The conflict has claimed the lives of tens of thousands of people and displaced around 3.3 million since 2015.
Two-thirds of the population - about 20 million people - require humanitarian support, according to the United Nations.
South Yemen was a separate state until it merged with the north in 1990.
Four years later, an armed secession bid ended in occupation by northern forces, giving rise to resentments which persist to this day.
A Saudi-led military coalition, which has backed pro-government forces against the Houthi rebels since 2015, sent a delegation to Aden last week to discuss the new front in the crisis.
In his address on Tuesday, Griffiths welcomed efforts by Saudi Arabia to convene a dialogue in Jeddah to discuss the current situation and resolve its difficulties.
Follow us on Twitter: @The_NewArab
Follow the Middle East's top stories in English at The New Arab on Google News
