The trial of six people among them former Sports CS Hassan Wario started on Monday with the prosecution promising to show how the officials mismanaged the team to Rio Olympics in 2016.
In her opening statement, senior principal prosecution counsel Maryanne Mwangi said they will be calling witnesses to show how the officials disregarded the law.
Ms Mwangi said a number of players went to the Games a little late because of so many changes in travel plans, which also led to loss of public funds.
Further, some athletes could not access the grounds in Rio de Janeiro, early enough, hampering their preparations.
"Good performance can only be achieved with proper planning and management," she said.
She said that in some instances, some athletes and officials were paid excess allowances while the management took joyriders, who had not been authorised to travel to Rio Olympics.
There was also irregular procurement of air travels, exceeding the budgeted amount.
Other than Dr Wario, former principal secretary Richard Ekai, Mr Haron Komen, Mr Stephen arap Soi, Mr Francis Kinyili Paul and Mr Patrick Kimathi Nkabu face 19 counts over Rio fiasco.
The charges include engaging in a project without prior planning, abuse of office, wilful failure to comply with applicable procedures and guidelines relating to management of public funds and fraudulent acquisition of public funds.
Ms Mwangi said the persons mandated to lead the delegation either varied or withdrew air travels, leading to wastage of public funds. She said the officials, who had the responsibility of ensuring prudent use of funds, failed to do so.
She said the fiasco created negative image for the country and lowered the spirit of many athletes.
The first witness, former National Olympic Committee Treasurer Fridah Shiroya said the event was marred with disorganisation.
Ms Shiroya said, despite having attended many events previously, the Rio Games was poorly planned.
She said upon arrival at such events, the officials would delegate duties among themselves but this was not the case in Rio. She said she wasn't given any role only to be ordered back home after staying in Rio for nine days.
"I was to stay in Rio for 19 days. But chef de mission (Mr Soi) told me to go back home. While there, I was supposed to assist the finance officer, sent by the government, but this never happened. The officer only assisted me in deporting someone," she said.
Ms Shiroya said she was never given an explanation but "coming home was a pleasure." She said that she was paid her allowance of about Sh1 million.