However, Tuwei said his failure to fill out the forms before the deadline led to the delay that saw him arrive in the US hours before his first race.
The agency played down claims that it prioritized facilitating government officials' travel to the United States over athletes.
"Allegations that persons other than athletes and support personnel illegally travelled to Oregon are false and unsubstantiated. Athletics Kenya hopes that this statement will set the record straight as a true account of the status of the Kenyan delegation in Oregon," read the statement.
The ministry has put in place a strict policy to ensure that only officials with specific roles accompany teams out of the country.
"The ministry has ensured that the athletes, national teams, and their support personnel are financed, adequately prepared, equipped, and facilitated in order to participate in international events, a practice that has contributed to the immense growth of sports, especially athletics," the body further stated.
Following the challenges, Omanyala failed to make it to the finals of the 100m race after finishing 5th in the semi-finals on Sunday.
The Africa 100m champion clocked a sluggish 10.14 secs missing out on the two automatic qualifying spots.
Kenya has tightened its oversight of domestic forex operations in recent years.