Mr Ruto and President Uhuru Kenyatta are charged separately with orchestrating a wave of violence that swept Kenya after contested elections in 2007, in which 1200 people died.
Several witnesses have withdrawn with prosecutors alleging intimidation.
The loss of a key witness led to the collapse of the case against Mr Kenyatta's co-accused, former civil service head Francis Muthaura, in March.
Prosecutors yesterday said Walter Osapiri Barasa had been charged with three counts of corruptly influencing a witness, allegedly paying one prosecution witness and her husband around £12,000 to withdraw testimony.
They said Kenya must now arrest Mr Barasa.
"This is the first case before the ICC where a suspect is charged with an offence against the administration of justice," the court said in its statement.
Mr Ruto's trial, which began last month, resumed on Wednesday, after an adjournment to allow the deputy president to handle issues related to the terror attack on a Nairobi mall.
Mr Kenyatta's trial starts in November.