Interior Minister Kithure Kindiki said the phased reopening of border posts in Mandera, Lamu and Garissa along the lengthy frontier with Somalia would not go ahead - as announced in May.
The decision comes after the murder of five civilians and the deaths of eight police officers in Kenya in separate incidents near the border last month blamed on al-Shabab.
"The government will delay the planned reopening of Kenya-Somalia border points until we conclusively deal with the recent spate of terror attacks and cross-border crime," Kindiki said during a visit to the Dadaab refugee camp in far eastern Kenya near Somalia.
The frontier was officially closed in October 2011 because of attacks by al-Shabab, which has been waging an insurgency against the central government in Mogadishu for more than 15 years.
The two nations had announced plans in July last year to reopen the border at talks between then Kenyan president Uhuru Kenyatta and his Somali counterpart Hassan Sheikh Mohamud but they never materialised.
But on May 15 this year, following a high-level ministerial meeting in Nairobi, officials from both countries agreed to the phased reopening of three border posts.
- 'Criminal elements' -
Mandera was to reopen within 30 days of the announcement, followed by Garissa in 60 days and Lamu in 90 days.
However on June 13, eight Kenyan police officers were killed in Garissa when their vehicle struck an improvised explosive device.
On June 24, five civilians had their throats cut in an attack in Lamu near the Somali border. Some were beheaded.
Kenya has suffered retaliatory attacks on its soil by al-Shabab since sending troops over the border into Somalia in 2011 to crush the al-Qaeda linked jihadists.
More than a decade later, Kenya is still a major contributor to an African Union force in Somalia trying to curb Al-Shabab's capacity to wage deadly attacks.
Among the deadliest attacks in Kenya was a massacre at Garissa University in 2015 that left 148 people dead, almost all of them students.
Two years earlier, 67 people were killed when militants stormed the Westgate shopping mall in Nairobi.
Kenya hosts tens of thousands of refugees at Dadaab, most of them Somalis fleeing violence, poverty and a ferocious drought over the border, and successive governments have voiced suspicion about some of those sheltering there.
Kindiki said "99.99 percent of refugees are good and law abiding and we will do our best to help them".
"However, there are few criminal elements who will not be allowed to hurt the interests of bona-fide refugees and the host communities," he said.