Dominican Republic Olympic Committee (COD) officials supposedly applied on the mistaken assumption that it was part of his separate application for the Pan American Sports Organization (PASO) Presidency.
This leaves Trinidad and Tobago's interim President Brian Lewis as the only candidate for the CANOC role as he bids to take up the job on a permanent basis.
The vote will take place at an Extraordinary General Assembly (EGM) tomorrow in Barranquilla, Colombia.
Puello's mistake has been explained in a letter sent to the CANOC Nominations Committee.
"We wish to apologise for the confusion with regards to the candidature sent in for Dr. José Joaquin Puello, and withdraw Dr. Puello's nomination for President of CANOC," explained the letter, seen by insidethegames, which was co-signed by COD President Luis Mejia Oviedo and secretary general Antonio Acosta.
It was added that they "mistook the CANOC nomination form as part of the procedures set for the PASO elections".
Puello's own signature was on the official nomination form which made clear it was an application for the position of CANOC President.
The application was sent out to every CANOC member on Monday (January 30).
insidethegames has repeatedly contacted Puello himself for clarification but has not yet received a response.
His PASO Presidential bid is thought to be unaffected.
The 76-year-old is one of five contenders to replace Julio Maglione as head of the regional bloc alongside Brazil's Carlos Nuzman, St Vincent and the Grenadines' Keith Joseph, Chile's Neven Ilic and St Lucia's Richard Peterkin.
An election is scheduled for April 26 in Uruguayan capital Montevideo.
Administrative errors are rare but not unheard of in sport.
In 2014, the International Cycling Union (UCI) missed the deadline to apply for inclusion at the Tokyo 2020 Paralympic Games.
UCI President Brian Cookson admitted they had "dropped the ball", but the sport was eventually included on the programme.
Lewis, President of the Trinidad and Tobago Olympic Committee (TTOC), was unanimously elected on an interim basis to replace Barbados' Steve Stoute as CANOC President at an Annual General Meeting in Guadeloupe in October.
The election is the only item on the EGM agenda for tomorrow.
Proceedings are beginning today in the Colombian coastal city with workshops run for delegates from the regional body.
Issues being discussed include "Good Governance and Financial Integrity" and "Human Trafficking in Sport".
Colombia is not a member of CANOC, but the organisation's meetings are taking place alongside the Central America and Caribbean Sport Organization General Assembly.