Mr Ruto has been charged with crimes against humanity, following allegations that he orchestrated violence after disputed elections in 2007.
Mr Ruto, the first serving official to appear at the ICC, denies the charge.
The court ruled the witness's identity, an alleged survivor of a church arson attack, should not be revealed.
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Kenya's violent elections
Clashes in the Mathare slum in Nairobi in January 2008
Then-President Mwai Kibaki declared the winner of December 2007 elections - Raila Odinga cries foul
Opposition protests lead to clashes with police and degenerate into ethnic violence across the country
Some 1,200 killed and 600,000 flee homes
Incumbent President Uhuru Kenyatta in Kibaki camp; accused of orchestrating violence against ethnic groups seen as pro-Odinga
Incumbent Deputy President William Ruto in Odinga camp; accused of targeting pro-Kibaki communities
Power-sharing deal signed in April 2008 after mediation by ex-UN chief Kofi Annan
Mr Kenyatta and Mr Ruto form alliance and win March 2013 election
Mr Ruto's trial started on 10 September; Mr Kenyatta's due in November
Q&A: Kenyan leaders at The Hague
Profile: Fatou Bensouda
Q&A: International Criminal Court
This was for her own safety and she will be known by the number 536.
Chief prosecutor Fatou Bensouda has previously said that witnesses have been intimidated in an attempt to prevent them from giving evidence.
Kenya's President Uhuru Kenyatta is due to stand trial in November. He also denies charges of fuelling violence after the 2007 election.
Some 1,200 people were killed and 600,000 forced from their homes in weeks of violence after the election.
More than 40,000 people are estimated to be still living in camps, which Mr Kenyatta has promised to close by 20 September.
He and Mr Ruto were on opposite sides during the 2007 election, but formed an alliance to win elections in March this year.
Analysts believe the ICC charges bolstered their campaign, as many Kenyans accused the court of interfering in Kenya's domestic affairs.
'Church attack'
Prosecutor Anton Steynberg told the court that "22 victims and witnesses, common Kenyan people, who will describe the attacks" would be called to testify in Mr Ruto's trial, Kenya's Daily Nation newspaper reports.
Mr Ruto is being charged alongside journalist Joshua arap Sang.
He is the head of a Kalenjin-language radio station and is accused of whipping up ethnic hatred - a charge he denies.
The first witness was a victim of an arson attack in January 2008 on the Kiambaa Church in Kenya's Rift Valley, one of the areas worst-affected by the violence.
Kenya"s Deputy President William Ruto (R) reacts as he sits in the courtroom before his trial at the International Criminal Court (ICC) in The Hague September 10, 2013.
William Ruto denies charges of murder, deportation and persecution
A mob set ablaze the church where people were taking refuge, burning 36 people beyond recognition.
The violence erupted after the opposition claimed that it had been robbed of victory.
It then took ethnic overtones, with Kenya's main groups - especially Kikuyus and Kalenjins - involved in attacks and reprisal attacks.
When Mr Ruto appeared in court last week, Ms Bensouda accused him of forming an "army" of Kalenjin youth to fight for power.
Mr Ruto's defence lawyer, Karim Khan, accused the prosecution of building its case on "a conspiracy of lies".
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