The Mahdi Army, al-Sadr's own force, is concentrated in both the areas.
Al-Sadr's threat came as at least eight people were reported killed and 22 others wounded in clashes on Sunday between joint US-Iraqi forces and Mahdi Army fighters in Sadr City, officials said.
Separately, nine university students and their driver were kidnapped near Baquba, north of Baghdad, when armed men stopped their vehicle at a fake checkpoint, police said.
The students were returning to Diyala university after a weekend break.
Meanwhile, the US military is claiming some 20 fighters were killed in overnight clashes in Baghdad. A military spokesman called it "the hottest night in weeks".
Three people were killed in one incident in northwestern Baghdad.
Residents of the Shula neighbourhood also said that missiles targeted and destroyed cars and homes.
The previous day, at least 13 people were killed and 80 injured in Sadr City as Iraqi soldiers backed by US and British forces battled militias both in this Baghdad locality and in the southern city of Basra.
Troops entered Basra's Hayaniya district and took control after several hours, Major-General Abdel Karim Khalaf, an interior ministry spokesman, said.
Al Jazeera's Owen Fay, reporting from Baghdad on Sunday, said that the underlying message that could be interpreted from al-Sadr's threat is that he wants to get back into the political process.
"He does not want to see his Shia rivals gaining influence in the country," Fay said.
"Violence could rapidly increase if al-Sadr continues this rhetoric, a clear indication that he still has political sway."
Sheikh Salah al-Obaidi, a spokesman for al-Sadr, told Al Jazeera that this is the last opportuniry of rthe iraqi government to make an effort to co-operate with the group.
He said: "We [the Sadrist movement] have tried and tried to improve the political situation in the country."
"But our calls were never heeded. This is the governments last chance to correct the current situation."
Amid the feuds within the Shia political camp, a leader of al-Qaeda in Iraq, an armed Sunni group, has announced that a one-month campaign will be launched, where the group will "offer the head of an American" as a gift to George Bush, the US president.
According to an audiotape made public on Saturday, Abu Hamza al-Muhajir, also known as Abu Ayyub al-Masri, made the announcement in a speech entitled The Paths to Victory, monitored by the SITE Intelligence Group.
The campaign, to be called Attack of Righteousness, was reportedly announced in "celebration" of the 4,000 US troops who have died in Iraq.
Al-Masri, who was born in Egypt, is regarded by US commanders as the real leader of al-Qaeda in Iraq although the group claims it is led by an Abu Omar al-Baghdadi, an Iraqi.
In the statement issued on Saturday, al-Sadr accused the Iraqi government of being too close to the US military.
"The occupation has made us target of its planes, tanks, air strikes and snipers. Without our support this government would not have been formed," he said.
"But with its alliance with the occupier [the Iraqi government] is not independent and sovereign as we would like it to be."
Hasan Kazemi Qomi, the Iranian ambassador to Iraq, also criticised the US military for raids in Sadr City.
"We are encouraging the [Iraqi] government to fight the outlaws," he said. "But we are against the way the Americans are implementing the policy by bombing and closing down Sadr City.
"In this way people are suffering. The wrong policy of Americans by bombing innocent people will yield bad results."
Iraqi security forces moved against Shia militia groups in Basra on March 25, on the order of Nuri al-Maliki, Iraq's prime minister, himself a Shia.
US and British forces gave reconnaissance and tactical support to the Iraqi military during the crackdown, which triggered clashes across Shia areas of Iraq, including Sadr City, al-Sadr's stronghold.
Although al-Sadr called his Mahdi Army fighters off the streets of Basra soon after the violence, raids by government forces have continued.
Hundreds of people have been killed and wounded since the operation.