This marks a sharp increase compared with the estimate by Health Minister Alejandro Gaviria on January 28, when he put the total number around 20,000, Xinhua reported.
Now, Colombia is the second worst-hit country influenced by Zika after Brazil, where the government said as many as 1.5 million people may have been infected.
The rise in Zika cases compounds fears about Zika in Colombia, especially concerning its links to the rise in Guillain-Barre syndrome (GBS) cases.
GBS is a rare condition which causes the body's immune system to aggressively attack the nervous system. While the fatality rate of GBS is normally around five percent, in serious cases it can cause paralysis in survivors.
On Tuesday, Colombia reported that nearly 100 cases of GBS have been reported across the country, with all these patients also suffering from Zika.
Three of these patients have died because of Zika virus infection and six more suspicious deaths were under investigation.
The World Health Organisation (WHO) and scientists around the world are racing to prove a link between Zika and rises in microcephaly and GBS.
If confirmed, it would provide a very unsettling new development for adult victims since the panic caused by Zika has mainly been due to babies born with microcephaly after their mothers became infected.
In a statement published on Friday about Zika in Colombia, the WHO explained 86 cases of GBS were reported in Colombia between mid-December and early February. All of these presented "symptoms compatible with Zika" while 94.8 percent of the 58 cases studied involved patients over 18 years old.
Also on Saturday, the WHO confirmed cases of GBS were also rising in Brazil, El Salvador, Suriname and Venezuela.
Stating that Zika has spread to 34 countries, the WHO issued a report saying "the cause of the increase in GBS... remains unknown, especially as dengue, chikungunya and Zika virus have all been circulating simultaneously in the Americas."
It also referred to a Zika outbreak in French Polynesia in 2013 and 2014, during which 42 GBS patients were all confirmed to have been infected with Zika.