The decision was taken at a high-level law and order meeting attended by President Gen Pervez Musharraf and Prime Minister Mir Zafarullah Khan Jamali.
They are the first to be declared terrorists under the new anti-law, a home ministry official said.
The home ministry said these individuals are operating from Pakistan and other foreign soil and involved in various acts of terrorism.
"If slogans are raised on reputed campuses for fragmenting India, resolutions are made to destroy it, and if Parliament attack convict Afzal Guru is hailed as a martyr, it is shameful and disconcerting," an appeal which has the consent of 33 individuals, including intellectuals and artistes, says.
Saeed-led JuD is the front organisation for the Lashkar-e-Tayiba which is responsible for carrying out the 2008 Mumbai attack that killed 166 people, including six Americans.
Security forces immediately cordoned off the area and launched search operations to track down the militants.
The Pakistani investigation team needs more evidence to take the investigation forward and hence, has written to the government to speak to India and apprise them of the situation.
Empowerment of the National Investigation Agency (NIA) with extra territorial jurisdiction and declaration of Maulana Masood Azhar, Hafiz Muhammad Saeed, Zakiur Rehman Lakhvi and Dawood Ibrahim as terrorists after legislative amendment were counted among its achievements by the MHA, headed by Union Home Minister Amit Shah.
Three persons with alleged "ideological leaning" towards the banned JeM were arrested in New Delhi for planning terror strikes in different parts of the national capital.
Gul is the sixth individual to have been designated as a terrorist by the Centre in the last fortnight.
Foreign Office spokesman Zahid Hafeez Chaudhri said on Thursday that "there was no pressure on Pakistan at all regarding the release of Wing Commander Abhinandan."
"No terrorist organisation will be allowed to derail the dialogue process between Pakistan and India," Pakistan's Defence Minister Khwaja Muhammad Asif was quoted as saying by the Radio Pakistan on Saturday.
As many as 313 fidayeens, out and about in Pakistan, plan to strike in India during the Lok Sabha elections.
Condemning the terror attack on the Pathankot air force base, China said it may have been launched "intentionally" to disrupt the momentum in Indo-Pak ties.
Senior government sources said the charge of carrying out a Pulwama scale terror attack bigger was given to the Jaish-e-Mohammed headed by Maulana Masood Azhar by Pakistan Army's Inter-Services Intelligence.
'ISI-backed jihadi groups like the Jaish-e-Mohammed and Lashkar-e-Tayiba are now prepared to cross the International Border and attack targets in Punjab at will,' says Ambassador G Parthasarathy, India's former high commissioner to Pakistan.
According to sources, the NIA is trying to collect more information like Jaish-e-Mohammad as a terrorist organisation and its role in the attack.
It is because of the feared domestic backlash that the Modi government is now stepping up pressure on Pakistan to accommodate Indian interests.
Singh said since Pakistan has given the assurance to the Indian government, there should be no reason to disbelieve them so early.
The visiting Pakistani JIT will begin recording the statements of the witnesses in the Pathankot terror attack case from Thursday.
An army soldier was also injured in the encounter.
After receiving sanction under Unlawful Activities (Prevention) Act, the NIA will name Azhar, his brother Rauf Asghar, and handlers of four terrorists -- Qashif Jan and Shaid Latif in the chargesheet to be filed soon, official sources said.
Pakistan on Wednesday arrested Jaish-e-Mohammad chief Maulana Masood Azhar, his brother and "several individuals" belonging to his dreaded outfit, which is suspected to have engineered the Pathankot terror attack, and sealed its offices after India demanded action, linking it to the fate of Foreign Secretary-level talks.
Although there has been no official word so far, it is unlikely that Foreign Secretary S Jaishankar would travel to Islamabd as planned this Thursday for talks with his Pakistani counterpart for the comprehensive bilateral dialogue.
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The government on Tuesday announced that only four terrorists had entered the Pathankot Air Force station to carry out the strike that left eight people dead. This is contrary to a statement made by Home Minister Rajnath Singh on March 4 when he had said that charred remains, apart from four bodies of terrorists, were found at the debris after security forces searched the Pathankot airforce station when the operation ended.
The mandates which Pakistan has failed include action against all United Nations-designated terrorists like Jaish-e-Mohammed chief Azhar, Lashker-e-Tayiba founder Hafiz Saeed and the outfit's operational commander Zakiur Rehman Lakhvi.
The fresh Red Corner notice was issued after the National Investigation Agency secured an 'open-ended' non-bailable warrant against Azhar and Rauf for allegedly conspiring to carry out terror strike on the strategic Indian Air Force base at Pathankot on the intervening night of January 1 and 2.
Maulana Masood Azhar was allowed to preach extremist ideology at several British mosques during a month-long visit to UK in 1993 on the invitation of Islamist scholars
Pakistani authorities have lodged a first information report into the Pathankot terror attack case, officials said on Friday.
Pakistan has not yet informed India whether it has taken any action taken against JeM, believed to be responsible for the terror attack on Pathankot airbase.
An National Investigation Agency court in Punjab on Tuesday issued proclamation notice against Pakistan-based terror outfit Jaish-e-Mohammed's chief Maulana Masood Azhar and three others, asking them to appear before it on March nine in connection with last year's brazen attack on Pathankot IAF base.
Pakistani media outlets on Sunday said the brazen attack by terrorists at a key Indian Air Force base will pose a "challenge to attempts to resurrect" the dialogue process between the two neighbours despite the goodwill generated by recent high-level meetings between their leaders.
Sharif questioned the stalled trial in the gruesome attack.
Sajjad Ahmed Khan, 27, a resident of Pulwama is also suspected to be involved in the conspiracy of Pulwama attacks.
"The killing of Abdul Rehman alias Fauji Bhai alias Fauji Baba, a Pakistani national, is a big success for security forces as he was a master in assembling improvised explosive devices for JeM," Inspector General of Police Vijay Kumar told reporters in Srinagar.
Pakistan failed to fulfil six of the 27 mandates so far as a result of which the country continues to be in the grey list of the FATF.