On Sunday, the leader of Yemen's Presidential Leadership Council, Rashad Al Alimi, met Egypt's ambassador to Yemen, Ahmad Farouq, after dozens of passengers were turned back for not meeting the new requirements.
Mr Farouq said the new rules did not target Yemenis specifically but “include several nationalities”.
Passengers said they were not informed of a last-minute change to entry requirements.
The measures mandate that Yemenis travelling for treatment in Egypt submit a medical report issued from within the country and not only from Yemen. The rules also shorten visit visa stays from six months to three.
Some framed his mismanagement of Yemen's relationship with Egypt as the reason for the new measures, especially after a recent trip he made to Ethiopia — a country with which Egypt is embroiled in a dispute over Addis Ababa's Great Ethiopian Renaissance Dam.
The move also drew a response from Yemen's Southern Transitional Council.
“What happened in Cairo airport to Yemeni passengers … is the responsibility of the foreign minister and the PLC has to remove him,” Hani bin Breik, deputy head of the STC, wrote on Twitter.
“Maybe this would fix the situation with Egypt, which has always been supportive and was a source of life for people,” he said.
Speaking to The National, Yemen's Deputy Human Rights Minister Majed Fadhil said there was “close co-ordination between the Egyptian and Yemeni foreign ministers”.
However, the passengers learnt of the rules only upon their arrival in Cairo, as suggested in videos and heard in voice clips recorded by travellers after they had landed.
“Nobody had informed us — I have family, some of them were allowed in and some of us weren't. It seems authorities just split us up into half and told us we can't enter. We don't even know why,” said Abdullah Hamid as he tried to find a seat on the plane's return flight to Aden.