Addressing a gathering of ministers and top officials in the Governor's House in the provincial capital of Quetta, Musharraf said India was behind the unrest in Balochistan.
India is providing arms and material support to those involved in violence in Balochistan, Musharraf was quoted as saying by TV news channels.
The President's comments came in the wake of a war of words between India and Pakistan on the suicide attack on the Indian embassy in Kabul, which New Delhi has blamed on Islamabad-based Inter-Services Intelligence agency.
Pakistan denied the charge while Prime Minister Yousuf Raza Gilani offered to investigate the allegation if India provided evidence in this regard.
Islamabad has for long blamed New Delhi for backing nationalist elements who are conducting a violent campaign in Balochistan for a greater say in the exploitation of the province's abundant natural resources, including minerals and gas.
These allegations had subsided in recent years, but Pakistani officials have repeated the charges following a recent spike in violence in Balochistan. The upsurge in attacks by Baloch nationalists coincided with the installation of a new provincial government led by the Pakistan People's Party.
Musharraf said some elements wanted law and order to deteriorate in Balochistan because they did not want development in the province. The government, he said, is determined to maintain peace in the province so that Balochistan could be brought at par with other parts of the country.
The Pakistani president condemned recent instances of targeted killings in Quetta and expressed concern at the deteriorating law and order situation in Balochistan.
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