The protest led to delay of several trains on this route.
Due to the blockade, Gorakhdam Express train could not leave Hisar while Rewari-Ganganagar train was stopped at Hansi station, railway authorities said.
Rewari bound Fazilka passenger train was stopped in Hisar till further orders, they said.
The protesters, led by their leader Hawa Singh, also held a rally near Bhagana village this morning and accused Haryana government for being "indifferent" towards their demand for reservation in jobs and educational institutions.
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He alleged the state government is not "serious" about Jat quota issue and they were being "ignored".
The BJP government in the state had earlier this week
formed a five-member committee, headed by Chief Secretary D S Dhesi, to hold talks with the agitating Jats.
Chief Minister Manohar Lal Khattar has said the talks between the government-appointed officers' panel and the Jats would continue in the second round and all points would be discussed.
During the fresh round of the agitation, the protesters have been staging dharnas at various places in the state amid elaborate security arrangements.
Security has been further strengthened in sensitive Rohtak district, officials said.
Last year, arsonists had also set fire to the Rohtak residence of Haryana's Finance Minister Abhimanyu.
In view of the fresh Jat stir, paramilitary forces have been deployed in sensitive areas, while the state police is maintaining a strict vigil.
Khattar had earlier said the government had accepted the demand of Jats of giving jobs to the next of kin of those who had lost their lives during the agitation last year.
As many as 30 people were killed and property worth crores of rupees was damaged at many places in Haryana during last year's Jat stir which had turned violent. However, this time the state has been put on maximum alert, the officials said.
Rohtak and some of its neighbouring districts, including Sonipat and Jhajjar, were the worst hit by the violence last year.