"It has nothing to do in our view with Israeli politics," White House spokesman Mike McCurry said of Mr Clinton's second meeting in three days with Mr Peres, enmeshed in a re-election campaign against Benjamin Netanyahu, leader of the right-wing Likud Party.
Mr Clinton and Mr Peres, who also met on Sunday, were to sign a counter- terrorism accord that formalises US support for Israel in combating guerrilla attacks such as the suicide bombings that killed 59 people in nine days in Israel.
When Mr Clinton visited Israel in March after attending an anti-terrorism summit of world leaders at Sharm el-Sheikh in Egypt, he pledged $100m (pounds 66m) in US assistance.
The accord arose from talks that Secretary of State Warren Christopher and CIA director John Deutch held with their Israeli counterparts in Jerusalem.
"It will put in place steps that we can take together with the government of Israel to combat terrorism and enhance the security of citizens in Israel but also the United States," Mr McCurry said.
The two leaders were also to discuss ways to move ahead the Middle East peace process in the wake of a US-brokered ceasefire between Israel and Hizbollah in southern Lebanon.
Mr Clinton's sessions with Mr Peres sparked charges in Israel that the President was openly campaigning for the Israeli Prime Minister.
Israel Channel Two TV called Mr Clinton's actions "an unprecedented mobilisation of support ... by a US president in favour of an electoral candidate in a democratic country".
Not so, said the White House. "The President would never attempt to interfere in the domestic political environment of another country," Mr McCurry said.