Al-Sadr supporters say they "absolutely reject" the agreement and have urged Iraqis to continue peaceful demonstrations against it.
Tens of thousands of Iraqis rallied against the deal on Friday.
Most of the protesters appeared to be followers of al-Sadr, whose Mahdi Army fought American and Iraqi troops in Baghdad's Sadr City district until a ceasefire agreement was signed earlier this month.
Al-Sadr has called for weekly protests in addition to the referendum against the security pact.
In recent days the Association of Muslim Scholars, Abdul-Aziz al-Hakim, one of Iraq's most powerful Shia politicians, and Grand Ayatollah Ali al-Sistani, a Shia spiritual leader, have all raised concerns about the proposed security deal.
The developments come as Ibrahim al-Jaafari, a former prime minister, launches a new political party, National Reform.
The party will take part in the next provincial elections under a separate list from the Dawa party, al-Jaafari said on Saturday.
George Bush, the US president, and Nuri al-Maliki, the Iraqi prime minister, signed a statement last December on the future of US-Iraqi relations.
Iraqi and US officials began negotiations in March on a blueprint for the long-term security agreement, and a second deal, to establish the legal basis for US troops to remain in the country after a UN mandate runs out.
Widespread opposition to the deal, however, has raised doubts that the deadline will be met.
Many Iraqis say Americans are seeking permanent bases in Iraq.
US officials have declined to comment on the talks until the draft is completed.
Meanwhile, the US military said a soldier died on Friday in a non-combat related incident.
The brings to 21 the total number of Americans killed in Iraq this month.
Sadr men stopped
Against this backdrop of fresh tensions, Nassar al-Rubaie, the leader of al-Sadr's bloc in the Iraqi parliament, was stopped on Saturday at a police checkpoint outside Diwaniya, south of Baghdad.
The six-car convoy, which was en route from Basra to the city of Najaf, was held up without reason for nearly two hours, al-Rubaie told the Associated Press news agency.
"We call upon the government to stop the harassment faced by the Sadrists every day and we demand that those responsible for this be tried," al-Rubaie said.
Asaad Ali, a Diwaniya police colonel, said al-Rubaie's armed guards had been stopped because police were under orders not to allow armed men into the city.
But he said a patrol was sent to escort the convoy on its way out of the province to Najaf.
In another development, Bernard Kouchner, the French foreign minister, arrived in the southern city of Nasiriya on Saturday for his second visit to Iraq in less than a year.
"This visit ... is a message of peace and co-operation and a chance to discuss any future French contribution to rebuilding Iraq," he said.
Kouchner, who is in Iraq for two days, held talks with Abel Abdul-Mahdi, the French-educated vice-president, and Aziz Kadhim Alwan, the provincial governor.
Kouchner is also due to inaugurate two new French consulates in Arbil in northern Iraq and Basra in the south.
France, which takes over the EU's rotating presidency in July, has said it will lead a drive for greater EU involvement in rebuilding Iraq and has offered to host reconciliation talks.