Kenya's flower farmers are facing tough times ahead as El Nino rains pound several parts of the country, which is set to adversely affect production.

The Kenya Flower Council (KFC) CEO Jane Ngige said the El Nino phenomenon will dampen the fortunes of flower exports.

"Greenhouse structures are also expected to be hard hit by strong winds causing an increase in production costs," Ngige said in a statement received on Wednesday.

Kenya's flower production now accounts for seven percent of the world's output, according to the latest statistics from the KFC.

And though the country is now ranked third after world leaders Colombia and Ecuador, the flower sector has had to face numerous challenges to register growth in the last couple of years, according to Ngige.

Ngige said that in 2014, production rose to 130,000 tonnes of flowers worth 560 million dollars from 120,000 tonnes worth 460 million dollars the previous year.

Ngige said transportation is expected to be affected as has happened in the past when major roads connecting the flower growing zones of the Moi South and North Lake Roads have been cut off from the main Nakuru-Nairobi highway used by exporters to take flowers to the Jomo Kenyatta International Airport.

The rains are expected to last into the early part of 2016, according to the Kenyan meteorological service. This will severely affect the flower industry in Kenya and the wider agricultural sector.

"We are expecting higher concentrations of disease, subdued production, disruption of transport and marooning of employees requiring we plan for emergency evacuations," said Oserian Development Company administration director Kirimi Mpungu.

Oserian is one of the leading companies exporting flowers in Kenya. Mpungu said the effects could spill over to the industry's most important annual flower sales season, Valentine's Day due to interruption of production cycles by the chilly weather, which inhibits productivity.

"We are not leaving anything to chance," Mpungu said, adding that the farm has cleared drainage trenches and is ready to pump out water if need arises.

The farm has also placed sandbags to redirect flood water and debris away from the farm, while the health center staff is on high alert in case of emergencies associated with flooding such as cholera, diarrhea, typhoid and malaria.

To keep the flowers lit and warm for continued growth, Oserian has introduced artificial lighting and heating in greenhouses to maintain the required light and temperatures to keep the flowers growing.