The Blues have been seeking to pay the transfer fee for Fernandez in instalments as they bid to stay in line with UEFA Financial Fair Play (FFP) rules.
But, according to reports in Portugal, Benfica have insisted that Chelsea meet the full value of his £105million release clause if they want to sign him this month.
Benfica want Fernandez to stay until the end of the season and it is unclear at this stage whether negotiations with Chelsea can be salvaged.
Fernandez has broadly agreed personal terms with Chelsea and wants to move to Stamford Bridge.
Chelsea remain keen to strengthen their midfield and have alternative targets, including Declan Rice and Jude Bellingham. But neither Rice nor Bellingham are available this month.
Should they miss out on Fernandez, Chelsea could turn their attempts to hijacking Arsenal’s move for Shakhtar Donetsk winger Mykhaylo Mudryk.
Shakhtar director Darijo Srna is set to be at Stamford Bridge for their game against Manchester City on Thursday.
Meanwhile, Chelsea are finalising a £33m move to sign Monaco defender Benoit Badiashile, who is set to be presented at Stamford Bridge ahead of the City game.