Anger has mounted since it emerged chief suspect Tunisian Anis Amri, 24 - who was shot dead Friday by police in Milan - was a known radical Islamist and criminal who had long been under counter-terrorism surveillance on suspicion he was plotting an attack.
Critics have also pointed to a two-day delay before authorities issued a public wanted notice for the fugitive, as well as the fact the rejected asylum seeker should have been deported long ago.
Amid the fierce criticism, Merkel pledged a "comprehensive" analysis of what went wrong.
"The Amri case raises questions - questions that are not only tied to this crime but also to the time before, since he came to Germany in July 2015" from Italy, she said.
"We will now intensively examine to what extent official procedures need to be changed."
Merkel said she had ordered justice and interior ministers at the federal and state level to "analyse every aspect of the case and present their conclusions as soon as possible" so that reforms, where needed, could be agreed and implemented quickly.
The German leader said she had also spoken with Tunisian President Beji Caid Essebsi by telephone to discuss anti-terror efforts and inform him that Germany would be "significantly accelerating" deportation of rejected asylum seekers.
Justice Minister Heiko Maas meanwhile pledged to examine "how to improve surveillance of potentially dangerous persons" and concrete steps to speed up deportations of illegal migrants.
Politicians and newspapers have deplored the fact that Amri had slipped through the net of security services, who knew he had been in contact with Islamist "hate preachers" and, according to news weekly Der Spiegel, that he had offered himself for a suicide mission.
German police had monitored Amri since March but dropped the surveillance in September thinking he was primarily as a small-time drug dealer.
Anger has also focused on the investigation since Monday's truck attack.
After following an initial false lead, police only found Amri's identity papers in the lorry's cabin a day after the attack, and authorities took another day before issuing a Europe-wide public wanted notice.
Merkel - already under fire from right-wing populists over her liberal migrant policies - can now expect the security debate to heat up ahead of an election expected in September.
Berlin's B.Z. tabloid charged in a blistering headline this week: "They knew him. They did nothing."
Conservative lawmaker Stephan Mayer said the case "held up a magnifying glass" to the failings of Merkel's migration policy, and Christian Lindner, head of the Free Democrats opposition party, charged that "catastrophic mistakes" had been made.
Peter Neumann, professor of security studies at the King's College, pointed to "a systemic failure", as security services lacked the manpower for around-the-clock surveillance of Germany's 550 known radical Islamists considered potentially violent.
"Germany's anti-terrorism structure is failing to match the scale of the problem," he said. "Once the dust settles, it will be important to have a fundamental rethink."
Islamist spy mole
German police can point to several attacks they have, or may have, prevented this year.
On Friday they said they detained two Kosovo-born brothers on suspicion they planned to attack a shopping centre in Oberhausen near the Dutch border.
But the security services have also suffered a number of embarrassing failures.
In October, Syrian bomb plot suspect Jaber al-Bakr escaped a police raid and was only caught thanks to the help of other refugees who apprehended and bound him.
Days after his arrest, he was found hanged in his cell.
And last month Germany's domestic spy service unmasked a Spanish-born agent in its own ranks as a suspected Islamist. Media reports said he was also a former gay porn actor.
Criticism has also focused on Germany's over-burdened asylum and immigration services.
Amri's asylum request was denied in June but because Tunisia refused to take him back, denying he was a citizen, he was issued a stay of deportation paper -- the document that police found in the mangled truck cabin.
The new Tunisian travel document only arrived on Wednesday, two days after the attack.
Germany has repeatedly accused Tunisia and other north African states of stalling on the repatriation of their nationals.
A law to designate Tunisia, as well as Morocco and Algeria, as "safe countries of origin", to raise the bar for asylum requests, has been held up for months in Germany's upper house, over human rights concerns in the North African countries.