Official Languages Commissioner Graham Fraser has agreed to look into the matter after a complaint from the New Democrats, who argue the order may violate the Official Languages Act.
The legislation guarantees the right of federal employees to work in their own language.
NDP MP Yvon Godin is pushing ahead with the complaint even though he says civil servants working for Fantino were told verbally last February that people who write to the department in French can receive a response in French.
The first directive was issued last July, shortly after Fantino was named to his current post in a cabinet shuffle.
The order was received by employees of the Canadian International Development Agency, says a staff member there who spoke to The Canadian Press on condition of anonymity.
The directive was withdrawn after it was questioned, the employee said, but was reissued — in English — in February.
"I would like to reiterate that ALL correspondence signed by the minister be sent in English," said the email from Fantino's office.
"In special cases, ie (Haitian Prime Minister Laurent) Lamothe, then it makes sense, but for example, for the Ethiopia trip thank you letters to staff, we noted twice that we had some in FR (French). I understand that we know the recipients first language is French however the minister can write in English if he chooses to do so."
Fantino was within his rights to do so under the Official Languages Act, the message noted.
But that didn't fly with Godin, the NDP spokesman on official languages.
"We're supposed to be a bilingual country," he said. "When the minister wants to sign letters in English and send his letters in English without regard to the official languages, there's a problem."
A spokeswoman for Fantino insisted the minister respected the official languages law.
"Minister Fantino respects and corresponds in both national languages, however in this instance he wished to send personalized thank you letters to a few officials," Meagan Murdoch, Fantino's director of communications, said in an email.
"The fact that anyone would criticize special recognition of hard working officials is simply disrespectful and tasteless."
A spokesman for Fraser's office would not comment on the specifics of the case until the investigation is completed.
"Is a unilingual letter to Ethiopian staff in accordance with the law?" asked Nelson Kalil. "That's what the investigation will determine.
"But in general, the correspondence of the department and the minister must be written in both official languages," he said. "We'll have a look at it."
The staffer who raised the alarm believes other questionable situations may arise again in terms of language use even if it is rare for a minister to address employees directly.
"It's kind of like fly fishing," the staffer said. "He throws the bait and sees if there's any response. When he gets a bit of a reaction, he backs off. But it always comes back."
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