The reason given was that the Pope was on holidays.
Senior Vatican sources told the BBC the Pope does not normally receive politicians on his annual holiday at the Castelgandolfo residence near Rome.
But one leading Italian newspaper said it was an evident snub by the Vatican towards the Bush administration.
The first reason given is the short shrift papal legate, Cardinal Pio Laghi, received when he tried to talk the US out of invading Iraq in 2003.
The second is the Vatican's displeasure at the US saying it is unable to protect the rights of Iraqi Christians.
Instead of meeting the Pope, Ms Rice had to make do with a telephone conversation with the Vatican's number two, Cardinal Tarcisio Bertone.
Pope refused to meet Rice - report (Herald Sun, 20/9/07)
Pope 'refused meeting with Rice' (BBC News, 19/9/07)
LINKS (not necessarily endorsed by Church Resources)
Condoleezza Rice (Wikipedia)
Israel apologises over cancelled Vatican meeting (CathNews, 30/3/07)
Venezuela bishop slams Rice "lies" (CathNews, 9/2/07)
Cardinal Sodano meets US Secretary of State Condoleezza Rice (CathNews, 9/2/05)