Some have complained about the lengthy queuing times and urged the government to find ways to prevent large crowds.
"It is obvious that two stores for a population of more than 250,000 farmers is a big joke. It is time to open stores in all the sub-counties," said Peter Cheruiyot.
Mr Cheruiyot said that delays in restocking fertiliser have also contributed to overcrowding. "This is a wake-up call to the national government to ensure fertiliser is stocked throughout the year."
Farmers now want county leader to fast-track the establishment of fertiliser stores in all sub-county headquarters to reduce overcrowding.
They said this will shorten the distances they travel to get fertilisers.
"The situation at the moment where we travel many kilometers to Bomet town to get inputs is costly and makes attempts to subsidize fertilizer worthless," said Cheruiyot.
"We are struggling to get fertilizer not because it is out of stock but because the distance and transportation costs are straining our resources."
John Bore from Chepalungu expressed concerns that the subsidy provided by the national government was losing its meaning due to the high travel costs.
Mr Bore said that many farmers are choosing to buy more expensive fertilizer because of the long distances they have to travel and the hassle of queuing.
However, Bomet Governor Hillary Barchok, during the launch of the ongoing farmer listing exercise, promised to address the issue of farmers traveling long distances to buy fertiliser from NCPB depots.