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The attacker detonated his explosive vest in a district of Paktika.
"As a result, three civilians were killed and 11 other civilians were wounded," the ministry said in a statement, adding that provincial police have launched an investigation.
There has been a recent spike in suicide bombings a key Taliban tactic in Afghanistan along with IEDs or home made bombs which are the main cause of casualties to Afghan and international troops in the country.
A limited withdrawal of foreign troops from seven relatively peaceful areas of the country is due to start in July.
Afghan forces are set to take increasing responsibility for security as foreign troops pull back.