Some 400 entrants from 14 countries had to be put up in Lagos hotels.
The African Athletics Championship in Nigeria have become a source of friction as competitors struggle to reach host city Asaba while some nations have given up and dropped out.
The schedule for the competition, running from August 1-5, has been reworked on a "when can you get here" basis as unhappy athletes have been held up at Abuja and Lagos airports, blocked by visa issues or a lack of flights.
Photos of the athletes sleeping on their luggage at the airports have flooded social media.
Some 400 entrants from 14 countries had to be put up in Lagos hotels. Kenya's 60-strong team camped at Lagos airport for two days. Neighbours Tanzania did not even bother sending their much smaller team and withdrew.
On Thursday, a huge water tank, built to supply a swimming pool that is still under construction, collapsed outside the stadium, crushing parked cars and increasing fears that facilities had been built in too much of a rush. Athletes have complained about a bumpy running track.
Solomon Ogba, chairman of the local organising committee, told a press conference on Thursday that after Nigeria won the right to hold the championships none of its regions wanted to act as host, and that the Delta State had taken the role to save the event.
The delays and travel problems have led to accusations and counter accusations.
The Tanzanians said organisers had sent out documents too late. Ogba said competing nations had sent travel plans too late.
The Kenyans complained about arrangements for the 430-kilometre flight from Lagos to Asaba.
"We are made to understand that the chaos was caused by the fact that the LOC had offered the charter flight services to just one company under the name 'Overland Airways' despite having many other options with many private companies operating."
The championships serve as the selection meet for the African team at the IAAF Intercontinental Cup in the Czech Republic in September.